R3C320 last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

chembl
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

Other names: chembl

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

Webpage:

https://www.ebi.ac.uk/chembl/

Licence:

Name: Creative Commons Attribution-ShareAlike v3.0
URL: https://chembl.gitbook.io/chembl-interface-documentation/about#data-licensing

Publications: (8)

Publications
More detailed information about this field from each metasource.

ChEMBL: a large-scale bioactivity database for drug discovery
PMID: 21948594
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

The ChEMBL database in 2017
PMID: 27899562
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

The ChEMBL bioactivity database: an update
PMID: 24214965
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

ChEMBL: towards direct deposition of bioassay data
PMID: 30398643
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr
PMID: 19194660
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

http://europepmc.org/articles/PMC5210557
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gkt1031
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

http://dx.doi.org/10.1093/nar/gkv1352
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

ChEMBL: a large-scale bioactivity database for drug discovery PubMed citations: 1041.

1041 articles citing: ChEMBL: a large-scale bioactivity database for drug discovery

SApredictor: An Expert System for Screening Chemicals Against Structural Alerts. PMID:35910729
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Development of New Potential Inhibitors of β1 Integrins through In Silico Methods-Screening and Computational Validation. PMID:35888022
Developing New Treatments for COVID-19 through Dual-Action Antiviral/Anti-Inflammatory Small Molecules and Physiologically Based Pharmacokinetic Modeling. PMID:35887353
The Molecular Mechanism of Traditional Chinese Medicine Prescription: Gu-tong Formula in Relieving Osteolytic Bone Destruction. PMID:35872837
Modern drug discovery applications for the identification of novel candidates for COVID-19 infections. PMID:35845863
Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency? PMID:35836119
Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches. PMID:35832613
Toward in Silico Modeling of Dynamic Combinatorial Libraries. PMID:35756377
Designing optimized drug candidates with Generative Adversarial Network. PMID:35754029
Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. PMID:35733108
Rings in Clinical Trials and Drugs: Present and Future. PMID:35730680
Computer-Assisted Discovery of Alkaloids with Schistosomicidal Activity. PMID:35723407
Improving Small Molecule pK a Prediction Using Transfer Learning With Graph Neural Networks. PMID:35721000
Exploration of the Mechanism of Salvianolic Acid for Injection Against Ischemic Stroke: A Research Based on Computational Prediction and Experimental Validation. PMID:35694259
Molecular Similarity Perception Based on Machine-Learning Models. PMID:35682792
A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. PMID:35677070
Language models can learn complex molecular distributions. PMID:35672310
InflamNat: web-based database and predictor of anti-inflammatory natural products. PMID:35659771
A survey on computational taste predictors. PMID:35637881
Network Pharmacology Approach for Medicinal Plants: Review and Assessment. PMID:35631398
IVIVE: Facilitating the Use of In Vitro Toxicity Data in Risk Assessment and Decision Making. PMID:35622645
Creation of targeted compound libraries based on 3D shape recognition. PMID:35608807
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. PMID:35594413
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. PMID:35579568
UnbiasedDTI: Mitigating Real-World Bias of Drug-Target Interaction Prediction by Using Deep Ensemble-Balanced Learning. PMID:35566330
Deep Probabilistic Learning Model for Prediction of Ionic Liquids Toxicity. PMID:35563648
Probing the origin of estrogen receptor alpha inhibition via large-scale QSAR study. PMID:35542807
Computational method for estimating progression saturation of analog series. PMID:35542404
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Discovery of Cobimetinib as a novel A-FABP inhibitor using machine learning and molecular docking-based virtual screening. PMID:35520131
An in silico pipeline for the discovery of multitarget ligands: A case study for epi-polypharmacology based on DNMT1/HDAC2 inhibition. PMID:35475037
Antiviral Efficacy of Selected Natural Phytochemicals against SARS-CoV-2 Spike Glycoprotein Using Structure-Based Drug Designing. PMID:35458599
Discovery of moiety preference by Shapley value in protein kinase family using random forest models. PMID:35428180
Novel and versatile artificial intelligence algorithms for investigating possible GHSR1α and DRD1 agonists for Alzheimer's disease. PMID:35423219
Repurposing Multiple-Molecule Drugs for COVID-19-Associated Acute Respiratory Distress Syndrome and Non-Viral Acute Respiratory Distress Syndrome via a Systems Biology Approach and a DNN-DTI Model Based on Five Drug Design Specifications. PMID:35409008
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Collaborative Approach between Explainable Artificial Intelligence and Simplified Chemical Interactions to Explore Active Ligands for Cyclin-Dependent Kinase 2. PMID:35382271
Novel drug-target interactions via link prediction and network embedding. PMID:35379165
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Fragment-based virtual screening discovers potential new Plasmodium PI4KIIIβ ligands. PMID:35331319
Artificial Intelligence Technologies for COVID-19 De Novo Drug Design. PMID:35328682
Extended continuous similarity indices: theory and application for QSAR descriptor selection. PMID:35288838
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. PMID:35283794
Application of deep metric learning to molecular graph similarity. PMID:35279188
Targeting the anti-apoptotic Bcl-2 family proteins: machine learning virtual screening and biological evaluation of new small molecules. PMID:35265218
PSnpBind: a database of mutated binding site protein-ligand complexes constructed using a multithreaded virtual screening workflow. PMID:35227289
DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer's Disease. PMID:35204697
PTML Modeling for Pancreatic Cancer Research: In Silico Design of Simultaneous Multi-Protein and Multi-Cell Inhibitors. PMID:35203699
Chemical Interrogation of Nuclear Size Identifies Compounds with Cancer Cell Line-Specific Effects on Migration and Invasion. PMID:35199530
S2DV: converting SMILES to a drug vector for predicting the activity of anti-HBV small molecules. PMID:35062019
A Review on Parallel Virtual Screening Softwares for High-Performance Computers. PMID:35056120
LEADD: Lamarckian evolutionary algorithm for de novo drug design. PMID:35033209
Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem. PMID:35013496
Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking. PMID:35010191
Multi-scale mechanism of antiviral drug-alike phytoligands from Ayurveda in managing COVID-19 and associated metabolic comorbidities: insights from network pharmacology. PMID:34993740
Comprehensive Analysis of Chemical Structures That Have Been Tested as CFTR Activating Substances in a Publicly Available Database CandActCFTR. PMID:34955819
EmbedDTI: Enhancing the Molecular Representations via Sequence Embedding and Graph Convolutional Network for the Prediction of Drug-Target Interaction. PMID:34944427
Antimalarial Drug Predictions Using Molecular Descriptors and Machine Learning against Plasmodium Falciparum. PMID:34944394
PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions. PMID:34938773
Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. PMID:34932340
Deep Learning Algorithms Achieved Satisfactory Predictions When Trained on a Novel Collection of Anticoronavirus Molecules. PMID:34912370
Synthon-based ligand discovery in virtual libraries of over 11 billion compounds. PMID:34912117
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Combined Pharmacophore and Grid-Independent Molecular Descriptors (GRIND) Analysis to Probe 3D Features of Inositol 1,4,5-Trisphosphate Receptor (IP3R) Inhibitors in Cancer. PMID:34884798
Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development. PMID:34872613
The Structural Determinants for α1-Adrenergic/Serotonin Receptors Activity among Phenylpiperazine-Hydantoin Derivatives. PMID:34834117
Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision. PMID:34814950
DaiCee: A database for anti-cancer compounds with targets and side effect profiles. PMID:34803258
Strategies to identify candidate repurposable drugs: COVID-19 treatment as a case example. PMID:34785660
Deep scaffold hopping with multimodal transformer neural networks. PMID:34774103
DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. PMID:34772471
V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization. PMID:34769065
Prediction of Anti-Glioblastoma Drug-Decorated Nanoparticle Delivery Systems Using Molecular Descriptors and Machine Learning. PMID:34768951
Img2Mol - accurate SMILES recognition from molecular graphical depictions. PMID:34760202
De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations. PMID:34739968
Learning from low-rank multimodal representations for predicting disease-drug associations. PMID:34736437
Artificial Intelligence, Machine Learning, and Deep Learning in Real-Life Drug Design Cases. PMID:34731478
Deep Learning in Structure-Based Drug Design. PMID:34731473
Deep Neural Networks for QSAR. PMID:34731472
Has Artificial Intelligence Impacted Drug Discovery? PMID:34731468
Deep Learning and Computational Chemistry. PMID:34731467
ScaffComb: A Phenotype-Based Framework for Drug Combination Virtual Screening in Large-Scale Chemical Datasets. PMID:34723439
BrainBase: a curated knowledgebase for brain diseases. PMID:34718720
Centrality of drug targets in protein networks. PMID:34715787
MEMES: Machine learning framework for Enhanced MolEcular Screening. PMID:34659706
Application of Computational Methods in Understanding Mutations in Mycobacterium tuberculosis Drug Resistance. PMID:34651013
Individual and collective human intelligence in drug design: evaluating the search strategy. PMID:34635158
Consensus Virtual Screening Identified [1,2,4]Triazolo[1,5-b]isoquinolines As MELK Inhibitor Chemotypes. PMID:34632716
A survey on computational methods in discovering protein inhibitors of SARS-CoV-2. PMID:34623382
Prediction and identification of synergistic compound combinations against pancreatic cancer cells. PMID:34585118
How can SHAP values help to shape metabolic stability of chemical compounds? PMID:34579792
Representation of molecules for drug response prediction. PMID:34571534
Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species. PMID:34570764
Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery. PMID:34554348
Chromosome-scale assembly and whole-genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets. PMID:34549895
A cross-study analysis of drug response prediction in cancer cell lines. PMID:34524425
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures. PMID:34507532
QSAR-Based Computational Approaches to Accelerate the Discovery of Sigma-2 Receptor (S2R) Ligands as Therapeutic Drugs. PMID:34500703
Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid Hormone Binding Proteins. PMID:34500576
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding. PMID:34479477
A review on machine learning approaches and trends in drug discovery. PMID:34471498
A computational study on hydroxychloroquine binding to target proteins related to SARS-COV-2 infection. PMID:34458558
Synthesis and Cytotoxic Activity of Combretastatin A-4 and 2,3-Diphenyl-2H-indazole Hybrids. PMID:34451912
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. PMID:34439361
Computational Drug Repurposing for Antituberculosis Therapy: Discovery of Multi-Strain Inhibitors. PMID:34439055
Non-β-Lactam Allosteric Inhibitors Target Methicillin-Resistant Staphylococcus aureus: An In Silico Drug Discovery Study. PMID:34438984
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. PMID:34412708
Comparative analysis of molecular fingerprints in prediction of drug combination effects. PMID:34401895
CardioTox net: a robust predictor for hERG channel blockade based on deep learning meta-feature ensembles. PMID:34399849
AI-Based Drug Discovery of TKIs Targeting L858R/T790M/C797S-Mutant EGFR in Non-small Cell Lung Cancer. PMID:34393769
Machine Learning in Drug Discovery: A Review. PMID:34393317
Machine learning approaches for drug combination therapies. PMID:34368832
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Prediction of antischistosomal small molecules using machine learning in the era of big data. PMID:34351547
Host metabolic reprogramming in response to SARS-CoV-2 infection: A systems biology approach. PMID:34333072
Identification of non-classical hCA XII inhibitors using combination of computational approaches for drug design and discovery. PMID:34330958
Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. PMID:34327214
Deep Learning Approach for Discovery of In Silico Drugs for Combating COVID-19. PMID:34326978
R-group replacement database for medicinal chemistry. PMID:34295541
Recent trends in artificial intelligence-driven identification and development of anti-neurodegenerative therapeutic agents. PMID:34282519
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge. PMID:34273053
Safe-in-Man Broad Spectrum Antiviral Agents. PMID:34258746
Covalent Antiviral Agents. PMID:34258745
An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19. PMID:34258282
Toward a Coronavirus Knowledge Graph. PMID:34209818
From Genome to Drugs: New Approaches in Antimicrobial Discovery. PMID:34177572
Regio-selectivity prediction with a machine-learned reaction representation and on-the-fly quantum mechanical descriptors. PMID:34163985
RTP4 is a novel prognosis-related hub gene in cutaneous melanoma. PMID:34154655
The application of artificial intelligence and data integration in COVID-19 studies: a scoping review. PMID:34151987
Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. PMID:34135888
Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. PMID:34131166
Target identification among known drugs by deep learning from heterogeneous networks. PMID:34123272
SyntaLinker: automatic fragment linking with deep conditional transformer neural networks. PMID:34123096
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19. PMID:34117734
Applications of artificial intelligence to drug design and discovery in the big data era: a comprehensive review. PMID:34110579
Machine learning models for classification tasks related to drug safety. PMID:34110577
A structure-kinetic relationship study using matched molecular pair analysis. PMID:34085042
Scaffold-based molecular design with a graph generative model. PMID:34084372
In silico drug repositioning using deep learning and comprehensive similarity measures. PMID:34074242
Prioritisation of Compounds for 3CLpro Inhibitor Development on SARS-CoV-2 Variants. PMID:34070140
Descriptors of Cytochrome Inhibitors and Useful Machine Learning Based Methods for the Design of Safer Drugs. PMID:34067565
Pretraining model for biological sequence data. PMID:34050350
Introducing the metacore concept for multi-target ligand design. PMID:34046634
Compound dataset and custom code for deep generative multi-target compound design. PMID:34046209
Exploring protein hotspots by optimized fragment pharmacophores. PMID:34045440
RNase P Inhibitors Identified as Aggregators. PMID:33972249
The peripheral and core regions of virus-host network of COVID-19. PMID:33956950
Identification of New Potential Inhibitors of Quorum Sensing through a Specialized Multi-Level Computational Approach. PMID:33946907
CSConv2d: A 2-D Structural Convolution Neural Network with a Channel and Spatial Attention Mechanism for Protein-Ligand Binding Affinity Prediction. PMID:33925310
In Silico Identification of Small Molecules as New Cdc25 Inhibitors through the Correlation between Chemosensitivity and Protein Expression Pattern. PMID:33918281
Synthesis, Antiprotozoal Activity, and Cheminformatic Analysis of 2-Phenyl-2H-Indazole Derivatives. PMID:33917871
VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds. PMID:33905509
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection. PMID:33892799
Arena3Dweb: interactive 3D visualization of multilayered networks. PMID:33885790
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders. PMID:33879050
Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors. PMID:33856768
Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. PMID:33856591
Multisubstituted pyrimidines effectively inhibit bacterial growth and biofilm formation of Staphylococcus aureus. PMID:33846401
Mutual Support of Ligand- and Structure-Based Approaches-To What Extent We Can Optimize the Power of Predictive Model? Case Study of Opioid Receptors. PMID:33799356
One-pot parallel synthesis of 1,3,5-trisubstituted 1,2,4-triazoles. PMID:33797670
QSAR Modeling for Multi-Target Drug Discovery: Designing Simultaneous Inhibitors of Proteins in Diverse Pathogenic Parasites. PMID:33777898
Phytochemicals from Ayurvedic plants as potential medicaments for ovarian cancer: an in silico analysis. PMID:33765217
Fragment-Based Drug Design of Selective HDAC6 Inhibitors. PMID:33759126
MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. PMID:33757283
In Silico Prediction of Fraction Unbound in Human Plasma from Chemical Fingerprint Using Automated Machine Learning. PMID:33748592
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES. PMID:33736687
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. PMID:33724022
Physicochemical Profiling and Comparison of Research Antiplasmodials and Advanced Stage Antimalarials with Oral Drugs. PMID:33718733
Integrating genomics with biomarkers and therapeutic targets to invigorate cardiovascular drug development. PMID:33707768
Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models. PMID:33676550
BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations. PMID:33659392
Discovering pathways in benign prostate hyperplasia: A functional genomics pilot study. PMID:33603850
Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. PMID:33603720
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions. PMID:33598870
De novo design of new chemical entities for SARS-CoV-2 using artificial intelligence. PMID:33590764
Drug repurposing for COVID-19 via knowledge graph completion. PMID:33571675
In Silico Studies of Lamiaceae Diterpenes with Bioinsecticide Potential against Aphis gossypii and Drosophila melanogaster. PMID:33540716
Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. PMID:33533614
Evaluating Deep Learning models for predicting ALK-5 inhibition. PMID:33508008
Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs. PMID:33507738
Exploring Novel Biologically-Relevant Chemical Space Through Artificial Intelligence: The NCATS ASPIRE Program. PMID:33501158
Low Basicity as a Characteristic for Atypical Ligands of Serotonin Receptor 5-HT2. PMID:33494248
Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. PMID:33448694
AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery. PMID:33441136
Type II Binders Targeting the "GLR-Out" Conformation of the Pseudokinase STRADα. PMID:33440120
Evaluation of deep and shallow learning methods in chemogenomics for the prediction of drugs specificity. PMID:33431042
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. PMID:33431038
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. PMID:33431036
QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. PMID:33431016
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. PMID:33431012
Transformer-CNN: Swiss knife for QSAR modeling and interpretation. PMID:33431004
SmartGraph: a network pharmacology investigation platform. PMID:33430980
Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT. PMID:33430978
Multi-task learning with a natural metric for quantitative structure activity relationship learning. PMID:33430958
A multiple classifier system identifies novel cannabinoid CB2 receptor ligands. PMID:33430920
In-silico protein-ligand docking studies against the estrogen protein of breast cancer using pharmacophore based virtual screening approaches. PMID:33424323
Brain Disease Network Analysis to Elucidate the Neurological Manifestations of COVID-19. PMID:33409839
Identification of Small Molecules Blocking the Pseudomonas aeruginosa type III Secretion System Protein PcrV. PMID:33406810
A unique ligand-steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure-based virtual screening. PMID:33386704
Biological Regulatory Network (BRN) Analysis and Molecular Docking Simulations to Probe the Modulation of IP3R Mediated Ca2+ Signaling in Cancer. PMID:33383780
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
In silico ranking of phenolics for therapeutic effectiveness on cancer stem cells. PMID:33371879
Application 2D Descriptors and Artificial Neural Networks for Beta-Glucosidase Inhibitors Screening. PMID:33333961
Bioactivity Comparison across Multiple Machine Learning Algorithms Using over 5000 Datasets for Drug Discovery. PMID:33325717
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
COVID-19 Knowledge Extractor (COKE): A Tool and a Web Portal to Extract Drug - Target Protein Associations from the CORD-19 Corpus of Scientific Publications on COVID-19. PMID:33269341
Identification of a Selective RelA Inhibitor Based on DSE-FRET Screening Methods. PMID:33266352
Network-based approach highlighting interplay among anti-hypertensives: target coding-genes: diseases. PMID:33214616
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
Repurposed drugs and nutraceuticals targeting envelope protein: A possible therapeutic strategy against COVID-19. PMID:33189776
In Silico Models to Predict the Perturbation of Molecular Initiating Events Related to Thyroid Hormone Homeostasis. PMID:33185102
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Learning to encode cellular responses to systematic perturbations with deep generative models. PMID:33159077
A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PMID:33156843
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
Data set of activity cliffs with single-atom modification and associated X-ray structure information for medicinal and computational chemistry applications. PMID:33088875
Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein-Inhibitor Complexes in Relevance to Developing Parkinson's Therapeutics. PMID:33081086
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction. PMID:33070179
DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology. PMID:33015739
Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. PMID:32993084
Quantitative Comparison of Three-Dimensional Activity Landscapes of Compound Data Sets Based upon Topological Features. PMID:32984733
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. PMID:32931270
Prediction of drug-target interactions from multi-molecular network based on LINE network representation method. PMID:32894154
Identification of New Targets and the Virtual Screening of Lignans against Alzheimer's Disease. PMID:32879651
Investigating Core Signaling Pathways of Hepatitis B Virus Pathogenesis for Biomarkers Identification and Drug Discovery via Systems Biology and Deep Learning Method. PMID:32878239
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. PMID:32779567
Generative Model for Proposing Drug Candidates Satisfying Anticancer Properties Using a Conditional Variational Autoencoder. PMID:32775866
Analyzing Active Constituents and Optimal Steaming Conditions Related to the Hematopoietic Effect of Steamed Panax notoginseng by Network Pharmacology Coupled with Response Surface Methodology. PMID:32775450
Plant-Based Phytochemicals as Possible Alternative to Antibiotics in Combating Bacterial Drug Resistance. PMID:32759771
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
Prediction of Antimalarial Drug-Decorated Nanoparticle Delivery Systems with Random Forest Models. PMID:32751710
Virtual Screening of C. Sativa Constituents for the Identification of Selective Ligands for Cannabinoid Receptor 2. PMID:32722631
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research. PMID:32715315
Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. PMID:32691011
Generative Network Complex for the Automated Generation of Drug-like Molecules. PMID:32686938
A Network Medicine Approach to Investigation and Population-based Validation of Disease Manifestations and Drug Repurposing for COVID-19. PMID:32676577
Machine Learning Platform to Discover Novel Growth Inhibitors of Neisseria gonorrhoeae. PMID:32661900
Virtual Screening of Human Class-A GPCRs Using Ligand Profiles Built on Multiple Ligand-Receptor Interactions. PMID:32652079
Key driver genes as potential therapeutic targets in renal allograft rejection. PMID:32634125
Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity. PMID:32611313
Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. PMID:32583000
Repositioning of 8565 Existing Drugs for COVID-19. PMID:32543196
X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists. PMID:32542862
Increasing the public activity cliff knowledge base with new categories of activity cliffs. PMID:32518687
Machine intelligence design of 2019-nCoV drugs. PMID:32511308
Simplified activity cliff network representations with high interpretability and immediate access to SAR information. PMID:32500478
Design of Dual Inhibitors of Histone Deacetylase 6 and Heat Shock Protein 90. PMID:32478236
SuFEx Activation with Ca(NTf2)2: A Unified Strategy to Access Sulfamides, Sulfamates, and Sulfonamides from S(VI) Fluorides. PMID:32459499
An up-to-date overview of computational polypharmacology in modern drug discovery. PMID:32452701
Structure-Based Virtual Screening: From Classical to Artificial Intelligence. PMID:32411671
Computational Methods for the Identification of Molecular Targets of Toxic Food Additives. Butylated Hydroxytoluene as a Case Study. PMID:32397407
Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. PMID:32371905
Advances in exploring activity cliffs. PMID:32367387
A Chemographic Audit of anti-Coronavirus Structure-activity Information from Public Databases (ChEMBL). PMID:32363750
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions. PMID:32361862
QSAR without borders. PMID:32356548
Application of MM-PBSA Methods in Virtual Screening. PMID:32340232
Selective Inhibition of Enterovirus A Species Members' Reproduction by Furano[2, 3-d]pyrimidine Nucleosides Revealed by Antiviral Activity Profiling against (+)ssRNA Viruses. PMID:32328513
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. PMID:32318354
Peptide-like and small-molecule inhibitors against Covid-19. PMID:32306822
A Focus on Unusual ECL2 Interactions Yields β2 -Adrenergic Receptor Antagonists with Unprecedented Scaffolds. PMID:32301583
Accelerated Discovery of Novel Ponatinib Analogs with Improved Properties for the Treatment of Parkinson's Disease. PMID:32292555
Cheminformatics Analysis and Modeling with MacrolactoneDB. PMID:32286395
MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. PMID:32237745
A Novel Sulfonyl-Based Small Molecule Exhibiting Anti-cancer Properties. PMID:32231565
How Sure Can We Be about ML Methods-Based Evaluation of Compound Activity: Incorporation of Information about Prediction Uncertainty Using Deep Learning Techniques. PMID:32210186
Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens. PMID:32197482
Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. PMID:32194980
Constrained Bayesian optimization for automatic chemical design using variational autoencoders. PMID:32190274
A deep learning-based method for drug-target interaction prediction based on long short-term memory neural network. PMID:32183788
The Glycine Receptor Allosteric Ligands Library (GRALL). PMID:32163115
Integrating computational lead optimization diagnostics with analog design and candidate selection. PMID:32140250
PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions. PMID:32123669
Deep Learning-driven research for drug discovery: Tackling Malaria. PMID:32069285
Heterogeneous Multi-Layered Network Model for Omics Data Integration and Analysis. PMID:32063919
A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder. PMID:32047432
Mechanism of tanshinones and phenolic acids from Danshen in the treatment of coronary heart disease based on co-expression network. PMID:32020855
The Roles of the NLRP3 Inflammasome in Neurodegenerative and Metabolic Diseases and in Relevant Advanced Therapeutic Interventions. PMID:32012695
Computational method for the identification of third generation activity cliffs. PMID:31993342
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. PMID:31971579
The role of human in the loop: lessons from D3R challenge 4. PMID:31965405
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Drug-target interaction prediction using Multi Graph Regularized Nuclear Norm Minimization. PMID:31945078
Machine-Learning-Assisted De Novo Design of Organic Molecules and Polymers: Opportunities and Challenges. PMID:31936321
In silico analysis of alternative splicing on drug-target gene interactions. PMID:31924844
Dihydroquinoline derivative as a potential anticancer agent: synthesis, crystal structure, and molecular modeling studies. PMID:31900682
Prioritization of novel ADPKD drug candidates from disease-stage specific gene expression profiles. PMID:31879244
A prospective compound screening contest identified broader inhibitors for Sirtuin 1. PMID:31863054
Biological representation of chemicals using latent target interaction profile. PMID:31861982
Efficient multi-objective molecular optimization in a continuous latent space. PMID:31853357
Cytotoxicity Of Chalcone Of Eugenia aquea Burm F. Leaves Against T47D Breast Cancer Cell Lines And Its Prediction As An Estrogen Receptor Antagonist Based On Pharmacophore-Molecular Dynamics Simulation. PMID:31807030
Construction of Quantitative Structure Activity Relationship (QSAR) Models to Predict Potency of Structurally Diversed Janus Kinase 2 Inhibitors. PMID:31805692
Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase. PMID:31738758
ContraDRG: Automatic Partial Charge Prediction by Machine Learning. PMID:31737032
PTS: a pharmaceutical target seeker. PMID:31725865
Network inference with ensembles of bi-clustering trees. PMID:31660848
Synthetic Activators of Cell Migration Designed by Constructive Machine Learning. PMID:31660283
An in silico Approach for Integrating Phenotypic and Target-based Approaches in Drug Discovery. PMID:31638744
Closing the Gap Between Therapeutic Use and Mode of Action in Remedial Herbs. PMID:31632273
Prediction of Passive Membrane Permeability by Semi-Empirical Method Considering Viscous and Inertial Resistances and Different Rates of Conformational Change and Diffusion. PMID:31609549
Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models. PMID:31584270
Towards precision medicine: interrogating the human genome to identify drug pathways associated with potentially functional, population-differentiated polymorphisms. PMID:31578463
Application of the Movable Type Free Energy Method to the Caspase-Inhibitor BindingAffinity Study. PMID:31569580
Chalcones as a basis for computer-aided drug design: innovative approaches to tackle malaria. PMID:31556721
Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors. PMID:31548507
A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments. PMID:31546814
Application of the SwissDrugDesign Online Resources in Virtual Screening. PMID:31540350
Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach. PMID:31530902
Evolving Concept of Activity Cliffs. PMID:31528788
Prognostic significance of TOP2A in non-small cell lung cancer revealed by bioinformatic analysis. PMID:31528121
Big Data and Artificial Intelligence Modeling for Drug Discovery. PMID:31518513
Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. PMID:31510073
Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies. PMID:31494804
Molecular Docking: Shifting Paradigms in Drug Discovery. PMID:31487867
Computational Drug Repurposing Algorithm Targeting TRPA1 Calcium Channel as a Potential Therapeutic Solution for Multiple Sclerosis. PMID:31480671
Promiscuous Ligands from Experimentally Determined Structures, Binding Conformations, and Protein Family-Dependent Interaction Hotspots. PMID:31459430
Systematic Extraction of Analogue Series from Large Compound Collections Using a New Computational Compound-Core Relationship Method. PMID:31459378
Rationalizing the Formation of Activity Cliffs in Different Compound Data Sets. PMID:31458921
Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. PMID:31453412
Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II. PMID:31434908
A rapid access to aliphatic sulfonyl fluorides. PMID:31434898
Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. PMID:31421629
Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis. PMID:31409761
Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods. PMID:31404334
Genetic Interaction-Based Biomarkers Identification for Drug Resistance and Sensitivity in Cancer Cells. PMID:31400611
NaPLeS: a natural products likeness scorer-web application and database. PMID:31399811
Screening of Drug Repositioning Candidates for Castration Resistant Prostate Cancer. PMID:31396486
Flavonoids from Brazilian Cerrado: Biosynthesis, Chemical and Biological Profile. PMID:31395797
Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2. PMID:31384471
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
A genome-wide positioning systems network algorithm for in silico drug repurposing. PMID:31375661
Evaluation and Identification of the Neuroprotective Compounds of Xiaoxuming Decoction by Machine Learning: A Novel Mode to Explore the Combination Rules in Traditional Chinese Medicine Prescription. PMID:31360720
Machine Learning From Molecular Dynamics Trajectories to Predict Caspase-8 Inhibitors Against Alzheimer's Disease. PMID:31354494
In silico comparative molecular docking analysis and analysis of the anti-inflammatory mechanisms of action of tanshinone from Salvia miltiorrhiza. PMID:31316608
Getting Docking into Shape Using Negative Image-Based Rescoring. PMID:31290660
Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs. PMID:31270468
Interoperable chemical structure search service. PMID:31254167
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. PMID:31236786
QSAR Classification Models for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer's Disease. PMID:31235739
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images. PMID:31218493
Rational design of novel sirtuin 1 activators via structure-activity insights from application of QSAR modeling. PMID:31217784
Leveraging Image-Derived Phenotypic Measurements for Drug-Target Interaction Predictions. PMID:31217689
Generative Topographic Mapping of the Docking Conformational Space. PMID:31216756
Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search. PMID:31207991
Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PMID:31206508
Why Some Targets Benefit from beyond Rule of Five Drugs. PMID:31188592
L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions. PMID:31182006
Error Tolerance of Machine Learning Algorithms across Contemporary Biological Targets. PMID:31167452
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. PMID:31127405
Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. PMID:31125569
AICD: an integrated anti-inflammatory compounds database for drug discovery. PMID:31123286
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
SLTChemDB: A database of chemical compounds present in Smokeless tobacco products. PMID:31073139
Identification of a Novel Bcl-2 Inhibitor by Ligand-Based Screening and Investigation of Its Anti-cancer Effect on Human Breast Cancer Cells. PMID:31057406
Revealing Drug-Target Interactions with Computational Models and Algorithms. PMID:31052598
Exploring the Potential of Spherical Harmonics and PCVM for Compounds Activity Prediction. PMID:31052500
Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds. PMID:31044166
Exploiting machine learning for end-to-end drug discovery and development. PMID:31000803
A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. PMID:30988527
Multistep Synthesis of 1,2,4-Oxadiazoles via DNA-Conjugated Aryl Nitrile Substrates. PMID:30964278
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. PMID:30963287
Network-based characterization of drug-protein interaction signatures with a space-efficient approach. PMID:30953486
Synthesis of Tri- and Difluoromethoxylated Compounds by Visible-Light Photoredox Catalysis. PMID:30943329
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity. PMID:30907586
Elucidating the druggability of the human proteome with eFindSite. PMID:30888556
Using genetic drug-target networks to develop new drug hypotheses for major depressive disorder. PMID:30877270
Exploring the GDB-13 chemical space using deep generative models. PMID:30868314
Network-based prediction of drug combinations. PMID:30867426
Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment. PMID:30846939
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. PMID:30839948
High-throughput screening and Bayesian machine learning for copper-dependent inhibitors of Staphylococcus aureus. PMID:30839007
DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. PMID:30835466
Systematic identification of target set-dependent activity cliffs. PMID:30828462
Identification of bioactive metabolites using activity metabolomics. PMID:30814649
Brazilian malaria molecular targets (BraMMT): selected receptors for virtual high-throughput screening experiments. PMID:30810604
Computational Drug Repositioning for Gastric Cancer using Reversal Gene Expression Profiles. PMID:30804389
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. PMID:30767155
A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine. PMID:30754631
Enhanced taxonomy annotation of antiviral activity data from ChEMBL. PMID:30753475
Multi-task generative topographic mapping in virtual screening. PMID:30739238
The Distribution of Standard Deviations Applied to High Throughput Screening. PMID:30718587
Avoiding hERG-liability in drug design via synergetic combinations of different (Q)SAR methodologies and data sources: a case study in an industrial setting. PMID:30712151
AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy. PMID:30669929
QBMG: quasi-biogenic molecule generator with deep recurrent neural network. PMID:30656426
The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method. PMID:30611214
MDAD: A Special Resource for Microbe-Drug Associations. PMID:30581775
Workflow for defining reference chemicals for assessing performance of in vitro assays. PMID:30570668
Multitarget Drug Design, Molecular Docking and PLIF Studies of Novel Tacrine-Coumarin Hybrids for the Treatment of Alzheimer's Disease. PMID:30568682
Development and Testing of Druglike Screening Libraries. PMID:30563329
Combining Ensemble Learning with a Fragment-Based Topological Approach To Generate New Molecular Diversity in Drug Discovery: In Silico Design of Hsp90 Inhibitors. PMID:30555986
Predicting protein targets for drug-like compounds using transcriptomics. PMID:30532261
An integrative machine learning approach for prediction of toxicity-related drug safety. PMID:30515477
Three-dimensional descriptors for aminergic GPCRs: dependence on docking conformation and crystal structure. PMID:30484023
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
The Varieties of the Psychedelic Experience: A Preliminary Study of the Association Between the Reported Subjective Effects and the Binding Affinity Profiles of Substituted Phenethylamines and Tryptamines. PMID:30467466
Application of Sequential Palladium Catalysis for the Discovery of Janus Kinase Inhibitors in the Benzo[ c]pyrrolo[2,3- h][1,6]naphthyridin-5-one (BPN) Series. PMID:30460842
BET bromodomain inhibitors: fragment-based in silico design using multi-target QSAR models. PMID:30421269
Systems-Mapping of Herbal Effects on Complex Diseases Using the Network-Perturbation Signatures. PMID:30405409
Scaffold-Hopping from Synthetic Drugs by Holistic Molecular Representation. PMID:30405170
ezCADD: A Rapid 2D/3D Visualization-Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. PMID:30403855
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
A large-scale dataset of in vivo pharmacology assay results. PMID:30351302
The Pioglitazone Trek via Human PPAR Gamma: From Discovery to a Medicine at the FDA and Beyond. PMID:30337873
In search of the representative pharmacophore hypotheses of the enzymatic proteome of Plasmodium falciparum: a multicomplex-based approach. PMID:30315397
Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation. PMID:30309962
Identification of novel acetylcholinesterase inhibitors designed by pharmacophore-based virtual screening, molecular docking and bioassay. PMID:30297729
Efficient multi-task chemogenomics for drug specificity prediction. PMID:30286165
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. PMID:30278128
Development of comprehensive data repository on chemicals present in smokeless tobacco products: Opportunities & challenges. PMID:30264748
Data-Driven Exploration of Selectivity and Off-Target Activities of Designated Chemical Probes. PMID:30249057
Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance. PMID:30247811
Designing novel inhibitors against Mycobacterium tuberculosis FadA5 (acetyl-CoA acetyltransferase) by virtual screening of known anti-tuberculosis (bioactive) compounds. PMID:30237678
Exploring Selectivity of Multikinase Inhibitors across the Human Kinome. PMID:30221217
Receptor pharmacophore ensemble (REPHARMBLE): a probabilistic pharmacophore modeling approach using multiple protein-ligand complexes. PMID:30220049
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. PMID:30219839
Machine Learning for Drug-Target Interaction Prediction. PMID:30200333
Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs. PMID:30192413
Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets. PMID:30190791
Rescoring of docking poses under Occam's Razor: are there simpler solutions? PMID:30173397
Binding site matching in rational drug design: algorithms and applications. PMID:30169563
Review of Drug Repositioning Approaches and Resources. PMID:30123072
Discovery of indoleamine 2,3-dioxygenase inhibitors using machine learning based virtual screening. PMID:30108982
Tracing compound pathways using chemical space networks. PMID:30108753
Dark chemical matter in public screening assays and derivation of target hypotheses. PMID:30108727
Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data. PMID:30090397
In silico prediction of hERG potassium channel blockage by chemical category approaches. PMID:30090371
Designing Algorithms To Aid Discovery by Chemical Robots. PMID:30062108
A systematic evaluation of analogs and automated read-across prediction of estrogenicity: A case study using hindered phenols. PMID:30057968
KampoDB, database of predicted targets and functional annotations of natural medicines. PMID:30046160
Multi-objective de novo drug design with conditional graph generative model. PMID:30043127
Add-On therapy with Chinese herb medicine Bo-Er-Ning capsule (BENC) improves outcomes of gastric cancer patients: a randomized clinical trial followed with bioinformatics-assisted mechanism study. PMID:30034946
Discovery of Retinoic Acid-Related Orphan Receptor γt Inverse Agonists via Docking and Negative Image-Based Screening. PMID:30023945
Combining Similarity Searching and Network Analysis for the Identification of Active Compounds. PMID:30023879
Reconciling Selectivity Trends from a Comprehensive Kinase Inhibitor Profiling Campaign with Known Activity Data. PMID:30023860
Diclofenac Identified as a Kynurenine 3-Monooxygenase Binder and Inhibitor by Molecular Similarity Techniques. PMID:30023839
X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. PMID:30023769
Application of a New Scaffold Concept for Computational Target Deconvolution of Chemical Cancer Cell Line Screens. PMID:30023635
Exploring Structural Relationships between Bioactive and Commercial Chemical Space and Developing Target Hypotheses for Compound Acquisition. PMID:30023563
Support Vector Machine Classification and Regression Prioritize Different Structural Features for Binary Compound Activity and Potency Value Prediction. PMID:30023518
Synthesis of Structurally Diverse N-Substituted Quaternary-Carbon-Containing Small Molecules from α,α-Disubstituted Propargyl Amino Esters. PMID:30011115
Network-based approach to prediction and population-based validation of in silico drug repurposing. PMID:30002366
ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy. PMID:29993812
Selectivity Challenges in Docking Screens for GPCR Targets and Antitargets. PMID:29990431
Construction of an integrated database for hERG blocking small molecules. PMID:29979714
Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching. PMID:29968097
Molecular basis of atypicality of bupropion inferred from its receptor engagement in nervous system tissues. PMID:29961917
A novel methodology on distributed representations of proteins using their interacting ligands. PMID:29949957
Interspecies comparison of putative ligand binding sites of human, rat and mouse P-glycoprotein. PMID:29936088
DPubChem: a web tool for QSAR modeling and high-throughput virtual screening. PMID:29904147
Polypharmacology Within the Full Kinome: a Machine Learning Approach. PMID:29888050
Changing Trends in Computational Drug Repositioning. PMID:29874824
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Performance of Machine Learning Algorithms for Qualitative and Quantitative Prediction Drug Blockade of hERG1 channel. PMID:29806042
Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. PMID:29799486
What Do You Get from DNA-Encoded Libraries? PMID:29795750
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Pharmaceutical Machine Learning: Virtual High-Throughput Screens Identifying Promising and Economical Small Molecule Inhibitors of Complement Factor C1s. PMID:29735903
Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis. PMID:29698608
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. PMID:29684165
Collection of analog series-based scaffolds from public compound sources. PMID:29682322
Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. PMID:29672063
Data Mining and Computational Modeling of High-Throughput Screening Datasets. PMID:29671272
SPIDR: small-molecule peptide-influenced drug repurposing. PMID:29661129
e-Bitter: Bitterant Prediction by the Consensus Voting From the Machine-Learning Methods. PMID:29651416
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. PMID:29642892
Uncovering the Mechanisms of Chinese Herbal Medicine (MaZiRenWan) for Functional Constipation by Focused Network Pharmacology Approach. PMID:29632490
Opportunities and obstacles for deep learning in biology and medicine. PMID:29618526
Deep Learning for Drug Design: an Artificial Intelligence Paradigm for Drug Discovery in the Big Data Era. PMID:29603063
MetStabOn-Online Platform for Metabolic Stability Predictions. PMID:29601530
Identification of potent and selective small molecule inhibitors of the cation channel TRPM4. PMID:29579323
The polo-like kinase 1 inhibitor volasertib synergistically increases radiation efficacy in glioma stem cells. PMID:29535822
The discovery of novel HDAC3 inhibitors via virtual screening and in vitro bioassay. PMID:29464997
Linear Regression QSAR Models for Polo-Like Kinase-1 Inhibitors. PMID:29443884
Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications. PMID:29442436
WDL-RF: predicting bioactivities of ligand molecules acting with G protein-coupled receptors by combining weighted deep learning and random forest. PMID:29432522
An integrated structure- and pharmacophore-based MMP-12 virtual screening. PMID:29423648
A desirability-based multi objective approach for the virtual screening discovery of broad-spectrum anti-gastric cancer agents. PMID:29420638
Decoys Selection in Benchmarking Datasets: Overview and Perspectives. PMID:29416509
Computational design of new molecular scaffolds for medicinal chemistry, part II: generalization of analog series-based scaffolds. PMID:29379641
Design of a tripartite network for the prediction of drug targets. PMID:29340865
Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers. PMID:29340835
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. PMID:29335872
Similarity search combined with docking and molecular dynamics for novel hAChE inhibitor scaffolds. PMID:29332299
A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders. PMID:29320554
Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures. PMID:29317676
Identification of New Potential APE1 Inhibitors by Pharmacophore Modeling and Molecular Docking. PMID:29307141
Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed. PMID:29300482
Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases. PMID:29290010
Thiopurine Drugs Repositioned as Tyrosinase Inhibitors. PMID:29283382
Structure based drug discovery for designing leads for the non-toxic metabolic targets in multi drug resistant Mycobacterium tuberculosis. PMID:29268770
Application of Generative Autoencoder in De Novo Molecular Design. PMID:29235269
BoBER: web interface to the base of bioisosterically exchangeable replacements. PMID:29234984
Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling. PMID:29204742
Ligand-free, palladacycle-facilitated Suzuki coupling of hindered 2-arylbenzothiazole derivatives yields potent and selective COX-2 inhibitors. PMID:29199735
MSBIS: A Multi-Step Biomedical Informatics Screening Approach for Identifying Medications that Mitigate the Risks of Metoclopramide-Induced Tardive Dyskinesia. PMID:29191560
Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. PMID:29190967
DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. PMID:29186331
Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. PMID:29172488
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
Are there physicochemical differences between allosteric and competitive ligands? PMID:29125840
Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors. PMID:29125553
Computational approaches to chemical hazard assessment. PMID:29101769
Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets. PMID:29096442
Structure-Based Design and Discovery of New M2 Receptor Agonists. PMID:29094937
Antithrombotic properties of JJ1, a potent and novel thrombin inhibitor. PMID:29093471
Evolutionarily Conserved Roles for Blood-Brain Barrier Xenobiotic Transporters in Endogenous Steroid Partitioning and Behavior. PMID:29091768
Assessing and predicting drug-induced anticholinergic risks: an integrated computational approach. PMID:29090085
Target-similarity search using Plasmodium falciparum proteome identifies approved drugs with anti-malarial activity and their possible targets. PMID:29088219
Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. PMID:29086195
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. PMID:29086168
Scaffold Hunter: a comprehensive visual analytics framework for drug discovery. PMID:29086162
Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data. PMID:29086090
Molecular de-novo design through deep reinforcement learning. PMID:29086083
An algorithm to identify functional groups in organic molecules. PMID:29086048
ChemSAR: an online pipelining platform for molecular SAR modeling. PMID:29086046
Biological substantiation of antipsychotic-associated pneumonia: Systematic literature review and computational analyses. PMID:29077727
Exhaustive sampling of the fragment space associated to a molecule leading to the generation of conserved fragments. PMID:29063731
The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. PMID:29062930
Comparing pharmacophore models derived from crystallography and NMR ensembles. PMID:29047011
Report and Application of a Tool Compound Data Set. PMID:29035535
Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach. PMID:29018348
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. PMID:28931921
Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds. PMID:28884009
Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks. PMID:28871390
Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. PMID:28831242
An integrative study to identify novel scaffolds for sphingosine kinase 1 inhibitors. PMID:28822281
Road Map for the Structure-Based Design of Selective Covalent HCV NS3/4A Protease Inhibitors. PMID:28815420
An Ameliorated Prediction of Drug-Target Interactions Based on Multi-Scale Discrete Wavelet Transform and Network Features. PMID:28813000
Structure-Affinity Relationships and Structure-Kinetics Relationships of Pyrido[2,1-f]purine-2,4-dione Derivatives as Human Adenosine A3 Receptor Antagonists. PMID:28806076
Reverse translation of adverse event reports paves the way for de-risking preclinical off-targets. PMID:28786378
The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models. PMID:28781990
NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. PMID:28775335
THPdb: Database of FDA-approved peptide and protein therapeutics. PMID:28759605
Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. PMID:28725477
Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. PMID:28699633
Identification of Histamine H3 Receptor Ligands Using a New Crystal Structure Fragment-based Method. PMID:28684785
Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited. PMID:28670471
Identification of potential trypanothione reductase inhibitors among commercially available β-carboline derivatives using chemical space, lead-like and drug-like filters, pharmacophore models and molecular docking. PMID:28656524
Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds? PMID:28623485
Drug repurposing for aging research using model organisms. PMID:28620943
Predicting anatomic therapeutic chemical classification codes using tiered learning. PMID:28617230
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations. PMID:28588237
Network mirroring for drug repositioning. PMID:28539121
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
Receptor-ligand molecular docking. PMID:28509958
Bioinformatics in translational drug discovery. PMID:28487472
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. PMID:28472422
Assessing Scaffold Diversity of Kinase Inhibitors Using Alternative Scaffold Concepts and Estimating the Scaffold Hopping Potential for Different Kinases. PMID:28467353
Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory. PMID:28453640
The evolution of logic circuits for the purpose of protein contact map prediction. PMID:28439455
Rational design of non-resistant targeted cancer therapies. PMID:28436422
Pyrano[2,3,4-cd]indole as a Scaffold for Selective Nonbasic 5-HT6R Ligands. PMID:28435524
Use of Graph Database for the Integration of Heterogeneous Biological Data. PMID:28416946
Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. PMID:28397808
The influence of the negative-positive ratio and screening database size on the performance of machine learning-based virtual screening. PMID:28384344
Structural features embedded in G protein-coupled receptor co-crystal structures are key to their success in virtual screening. PMID:28380046
QSAR modeling and chemical space analysis of antimalarial compounds. PMID:28374255
Drug repurposing from the perspective of pharmaceutical companies. PMID:28369768
The druggable genome and support for target identification and validation in drug development. PMID:28356508
Structure-Based Discovery of New Antagonist and Biased Agonist Chemotypes for the Kappa Opioid Receptor. PMID:28339199
Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking. PMID:28323889
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. PMID:28296354
WONKA and OOMMPPAA: analysis of protein-ligand interaction data to direct structure-based drug design. PMID:28291763
Docking-based virtual screening of Brazilian natural compounds using the OOMT as the pharmacological target database. PMID:28285443
MOST: most-similar ligand based approach to target prediction. PMID:28284192
Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. PMID:28274840
The polypharmacology browser: a web-based multi-fingerprint target prediction tool using ChEMBL bioactivity data. PMID:28270862
Binding mode of triazole derivatives as aromatase inhibitors based on docking, protein ligand interaction fingerprinting, and molecular dynamics simulation studies. PMID:28255310
Chemistry-based molecular signature underlying the atypia of clozapine. PMID:28221369
Intramolecular Hydrogen Bond Expectations in Medicinal Chemistry. PMID:28197301
Fragment-based in silico modeling of multi-target inhibitors against breast cancer-related proteins. PMID:28194627
Representing high throughput expression profiles via perturbation barcodes reveals compound targets. PMID:28182661
Large-scale bioactivity analysis of the small-molecule assayed proteome. PMID:28178331
Drug-target interaction prediction via class imbalance-aware ensemble learning. PMID:28155697
Investigating the antiplasmodial activity of primary sulfonamide compounds identified in open source malaria data. PMID:28129569
Analog series-based scaffolds: computational design and exploration of a new type of molecular scaffolds for medicinal chemistry. PMID:28116132
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics. PMID:28071740
Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists. PMID:28061508
From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. PMID:28055203
Chembench: A Publicly Accessible, Integrated Cheminformatics Portal. PMID:28045544
Carbamate Insecticides Target Human Melatonin Receptors. PMID:28027439
Quantitative Structure-activity Relationship (QSAR) Models for Docking Score Correction. PMID:28001004
Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information. PMID:27990817
Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets. PMID:27982302
DNA-encoded chemistry: enabling the deeper sampling of chemical space. PMID:27932801
The ChEMBL database in 2017. PMID:27899562
Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. PMID:27869685
Bioinformatics and Drug Discovery. PMID:27848897
Empowering pharmacoinformatics by linked life science data. PMID:27830428
Harnessing Big Data for Systems Pharmacology. PMID:27814027
Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D). PMID:27812030
Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. PMID:27810775
Data-driven approaches used for compound library design, hit triage and bioactivity modeling in high-throughput screening. PMID:27789427
Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. PMID:27736015
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies. PMID:27722817
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. PMID:27696240
Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula. PMID:27678063
To Unveil the Molecular Mechanisms of Qi and Blood through Systems Biology-Based Investigation into Si-Jun-Zi-Tang and Si-Wu-Tang formulae. PMID:27677604
Polypharmacology in Precision Oncology: Current Applications and Future Prospects. PMID:27669965
In silico prediction of chemical mechanism of action via an improved network-based inference method. PMID:27646592
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. PMID:27629350
ROCS-derived features for virtual screening. PMID:27624668
Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization. PMID:27606011
Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking. PMID:27602288
Discovery of potent NEK2 inhibitors as potential anticancer agents using structure-based exploration of NEK2 pharmacophoric space coupled with QSAR analyses. PMID:27599492
Insight into drug resistance mechanisms and discovery of potential inhibitors against wild-type and L1196M mutant ALK from FDA-approved drugs. PMID:27585676
On the origins of three-dimensionality in drug-like molecules. PMID:27572621
Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway. PMID:27567076
Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies. PMID:27561920
Systematic selection of small molecules to promote differentiation of embryonic stem cells and experimental validation for generating cardiomyocytes. PMID:27551501
Structure-based discovery of opioid analgesics with reduced side effects. PMID:27533032
Large-scale ligand-based predictive modelling using support vector machines. PMID:27516811
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. PMID:27515740
Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure. PMID:27515428
LigandBox: A database for 3D structures of chemical compounds. PMID:27493549
Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity. PMID:27490970
Identification of Novel Smoothened Ligands Using Structure-Based Docking. PMID:27490099
Repurposing FDA-approved drugs for anti-aging therapies. PMID:27484416
Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? PMID:27482722
Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PMID:27467773
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
A Rational Approach for the Identification of Non-Hydroxamate HDAC6-Selective Inhibitors. PMID:27404291
Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem. PMID:27398098
Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies. PMID:27375423
bioassayR: Cross-Target Analysis of Small Molecule Bioactivity. PMID:27367556
Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource. PMID:27345761
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data. PMID:27303447
An Algorithm to Identify Target-Selective Ligands - A Case Study of 5-HT7/5-HT1A Receptor Selectivity. PMID:27271158
A human genome-wide loss-of-function screen identifies effective chikungunya antiviral drugs. PMID:27177310
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. PMID:27161010
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries. PMID:27154487
Ligand cluster-based protein network and ePlatton, a multi-target ligand finder. PMID:27143991
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. PMID:27141091
Inhibitor Discovery for the Human GLUT1 from Homology Modeling and Virtual Screening. PMID:27128978
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening. PMID:27110292
Trisubstituted-Imidazoles Induce Apoptosis in Human Breast Cancer Cells by Targeting the Oncogenic PI3K/Akt/mTOR Signaling Pathway. PMID:27097161
Pharmit: interactive exploration of chemical space. PMID:27095195
Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. PMID:27083051
Determining the Degree of Promiscuity of Extensively Assayed Compounds. PMID:27082988
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics. PMID:27075578
Modern approaches to accelerate discovery of new antischistosomal drugs. PMID:27073973
Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes. PMID:26989424
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. PMID:26989145
Peptide aptamer identified by molecular docking targeting translationally controlled tumor protein in leukemia cells. PMID:26972431
In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PMID:26963248
Harnessing publicly available genetic data to prioritize lipid modifying therapeutic targets for prevention of coronary heart disease based on dysglycemic risk. PMID:26946290
Lessons learned from the design of chemical space networks and opportunities for new applications. PMID:26945865
Identification of New Human Malaria Parasite Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors by Pharmacophore and Structure-Based Virtual Screening. PMID:26915022
CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. PMID:26908244
μ Opioid receptor: novel antagonists and structural modeling. PMID:26888328
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. PMID:26872142
Supporting read-across using biological data. PMID:26863516
Global analysis of publicly available safety data for 9,801 substances registered under REACH from 2008-2014. PMID:26863090
Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique. PMID:26851083
Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking. PMID:26845440
Self Organizing Map-Based Classification of Cathepsin k and S Inhibitors with Different Selectivity Profiles Using Different Structural Molecular Fingerprints: Design and Application for Discovery of Novel Hits. PMID:26840291
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. PMID:26829384
Chemoinformatics: Achievements and Challenges, a Personal View. PMID:26828468
Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. PMID:26808821
Application of Bioactive Natural Materials-based Products on Five Women's Diseases. PMID:26793675
COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS. PMID:26776170
Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses. PMID:26750305
A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PMID:26735851
Historeceptomic Fingerprints for Drug-Like Compounds. PMID:26733872
Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis. PMID:26713275
Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases. PMID:26703541
Distinctive Behaviors of Druggable Proteins in Cellular Networks. PMID:26699810
Design of chemical space networks on the basis of Tversky similarity. PMID:26695392
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
Privacy-preserving search for chemical compound databases. PMID:26678650
canSAR: an updated cancer research and drug discovery knowledgebase. PMID:26673713
Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. PMID:26657081
The Haemonchus contortus kinome--a resource for fundamental molecular investigations and drug discovery. PMID:26644012
ONRLDB--manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery. PMID:26637529
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
Repositioning of Thiourea-Containing Drugs as Tyrosinase Inhibitors. PMID:26633377
Exploring molecular variation in Schistosoma japonicum in China. PMID:26621075
Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. PMID:26607293
Large-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4. PMID:26596901
Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads. PMID:26583052
Target enhanced 2D similarity search by using explicit biological activity annotations and profiles. PMID:26583046
SureChEMBL: a large-scale, chemically annotated patent document database. PMID:26582922
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases. PMID:26579214
Extremely Randomized Machine Learning Methods for Compound Activity Prediction. PMID:26569196
Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds. PMID:26564142
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. PMID:26550826
Predicting Drug-Target Interactions via Within-Score and Between-Score. PMID:26543857
Potential Compounds for Oral Cancer Treatment: Resveratrol, Nimbolide, Lovastatin, Bortezomib, Vorinostat, Berberine, Pterostilbene, Deguelin, Andrographolide, and Colchicine. PMID:26536350
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. PMID:26516187
A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes. PMID:26507230
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Target prediction utilising negative bioactivity data covering large chemical space. PMID:26500705
PDB-Explorer: a web-based interactive map of the protein data bank in shape space. PMID:26493835
ZINC 15--Ligand Discovery for Everyone. PMID:26479676
Dark chemical matter as a promising starting point for drug lead discovery. PMID:26479441
Modeling enzyme-ligand binding in drug discovery. PMID:26457119
From drug response profiling to target addiction scoring in cancer cell models. PMID:26438695
Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays. PMID:26431201
PyMine: a PyMOL plugin to integrate and visualize data for drug discovery. PMID:26429562
Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures. PMID:26419860
Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data. PMID:26415647
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib. PMID:26403354
Identifying problematic drugs based on the characteristics of their targets. PMID:26388775
To Hit or Not to Hit, That Is the Question - Genome-wide Structure-Based Druggability Predictions for Pseudomonas aeruginosa Proteins. PMID:26360059
ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery. PMID:26356902
An eigenvalue transformation technique for predicting drug-target interaction. PMID:26350590
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules. PMID:26322135
Optimizing drug-target interaction prediction based on random walk on heterogeneous networks. PMID:26300984
An Aggregation Advisor for Ligand Discovery. PMID:26295373
Discovery and resupply of pharmacologically active plant-derived natural products: A review. PMID:26281720
Prediction of human population responses to toxic compounds by a collaborative competition. PMID:26258538
Interference of Bilirubin in the Determination of Magnesium with Methyl Thymol Blue. PMID:26244045
SerpentinaDB: a database of plant-derived molecules of Rauvolfia serpentina. PMID:26238452
Synergy Maps: exploring compound combinations using network-based visualization. PMID:26236402
Visualization of multi-property landscapes for compound selection and optimization. PMID:26233785
PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. PMID:26225536
Network-Based Analysis of Nutraceuticals in Human Hepatocellular Carcinomas Reveals Mechanisms of Chemopreventive Action. PMID:26225263
PhIN: A Protein Pharmacology Interaction Network Database. PMID:26225242
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
A One Pot Synthesis of Novel Bioactive Tri-Substitute-Condensed-Imidazopyridines that Targets Snake Venom Phospholipase A2. PMID:26196520
Chemical databases: curation or integration by user-defined equivalence? PMID:26194583
A large-scale crop protection bioassay data set. PMID:26175909
The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets. PMID:26155308
PubChem structure-activity relationship (SAR) clusters. PMID:26150895
SInCRe-structural interactome computational resource for Mycobacterium tuberculosis. PMID:26130660
Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. PMID:26121262
Antibiotic-modifying activity of riachin, a non-cyanogenic cyanoglycoside extracted from Bauhinia pentandra. PMID:26109849
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. PMID:26106450
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. PMID:26100629
SANCDB: a South African natural compound database. PMID:26097510
Many InChIs and quite some feat. PMID:26081259
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more. PMID:26075027
Promiscuity progression of bioactive compounds over time. PMID:26064479
A multi-label approach to target prediction taking ligand promiscuity into account. PMID:26064191
Quantitative Structure-Antioxidant Activity Models of Isoflavonoids: A Theoretical Study. PMID:26062128
Comprehensive prediction of drug-protein interactions and side effects for the human proteome. PMID:26057345
Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity. PMID:26049785
Fragment virtual screening based on Bayesian categorization for discovering novel VEGFR-2 scaffolds. PMID:26022686
Design and Validation of FRESH, a Drug Discovery Paradigm Resting on Robust Chemical Synthesis. PMID:26005525
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. PMID:25994950
Application of RNAi to Genomic Drug Target Validation in Schistosomes. PMID:25992548
The relationship between target-class and the physicochemical properties of antibacterial drugs. PMID:25975639
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. PMID:25971743
Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study. PMID:25949744
Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules. PMID:25926892
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. PMID:25925353
Structure-based predictions of activity cliffs. PMID:25918827
Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2. PMID:25916906
Predicting drug metabolism: experiment and/or computation? PMID:25907346
Creation of a free, Internet-accessible database: the Multiple Target Ligand Database. PMID:25897329
In silico identification of targets for a novel scaffold, 2-thiazolylimino-5-benzylidin-thiazolidin-4-one. PMID:25894361
ChEMBL web services: streamlining access to drug discovery data and utilities. PMID:25883136
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. PMID:25855807
Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PMID:25826798
Novel scaffolds for modulation of TRPV1 identified with pharmacophore modeling and virtual screening. PMID:25826358
Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. PMID:25815062
Recognition of chemical entities: combining dictionary-based and grammar-based approaches. PMID:25810767
Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation. PMID:25799414
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape. PMID:25776023
Bioisosteric matrices for ligands of serotonin receptors. PMID:25772514
Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts. PMID:25760829
Clostridium difficile drug pipeline: challenges in discovery and development of new agents. PMID:25760275
Multi-output model with Box-Jenkins operators of linear indices to predict multi-target inhibitors of ubiquitin-proteasome pathway. PMID:25754075
Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints. PMID:25750664
Systematic artifacts in support vector regression-based compound potency prediction revealed by statistical and activity landscape analysis. PMID:25742011
Therapeutic opportunities within the DNA damage response. PMID:25709118
Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling. PMID:25705261
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. PMID:25690787
Computational polypharmacology analysis of the heat shock protein 90 interactome. PMID:25686391
Flexibility and small pockets at protein-protein interfaces: New insights into druggability. PMID:25662442
Homology modeling, molecular dynamic simulation, and docking based binding site analysis of human dopamine (D4) receptor. PMID:25650117
Genetic blueprint of the zoonotic pathogen Toxocara canis. PMID:25649139
Structural insight into tetrameric hTRPV1 from homology modeling, molecular docking, molecular dynamics simulation, virtual screening, and bioassay validations. PMID:25642729
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. PMID:25638808
Comparative modeling and benchmarking data sets for human histone deacetylases and sirtuin families. PMID:25633490
Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor. PMID:25625646
Evaluation of 11 scoring functions performance on matrix metalloproteinases. PMID:25610645
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. PMID:25609831
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
TINAGL1 and B3GALNT1 are potential therapy target genes to suppress metastasis in non-small cell lung cancer. PMID:25521548
Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. PMID:25520777
Implementing the "Best Template Searching" tool into Adenosiland platform. PMID:25505667
Benchmarking methods and data sets for ligand enrichment assessment in virtual screening. PMID:25481478
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
Design and characterization of chemical space networks for different compound data sets. PMID:25465052
LigDig: a web server for querying ligand-protein interactions. PMID:25433696
Predicting targets of compounds against neurological diseases using cheminformatic methodology. PMID:25425329
Parallel worlds of public and commercial bioactive chemistry data. PMID:25415348
Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping. PMID:25407367
Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification. PMID:25374366
Covalent docking of large libraries for the discovery of chemical probes. PMID:25344815
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Sequential application of ligand and structure based modeling approaches to index chemicals for their hH4R antagonism. PMID:25330207
Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. PMID:25326818
Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling. PMID:25320644
EU-OPENSCREEN-chemical tools for the study of plant biology and resistance mechanisms. PMID:25320643
InCHlib - interactive cluster heatmap for web applications. PMID:25264459
Prediction of multi-target networks of neuroprotective compounds with entropy indices and synthesis, assay, and theoretical study of new asymmetric 1,2-rasagiline carbamates. PMID:25255029
OOMMPPAA: a tool to aid directed synthesis by the combined analysis of activity and structural data. PMID:25244105
Chemical biology strategies for posttranslational control of protein function. PMID:25237866
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. PMID:25221628
Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants. PMID:25195622
BioModels linked dataset. PMID:25182954
LBVS: an online platform for ligand-based virtual screening using publicly accessible databases. PMID:25182364
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. PMID:25165633
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening. PMID:25165489
Curation and analysis of multitargeting agents for polypharmacological modeling. PMID:25133604
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Composition and applications of focus libraries to phenotypic assays. PMID:25104937
Evolving BioAssay Ontology (BAO): modularization, integration and applications. PMID:25093074
PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers. PMID:25075287
Computational methods for analysis and inference of kinase/inhibitor relationships. PMID:25071826
The Protein Data Bank archive as an open data resource. PMID:25062767
Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods. PMID:25058446
Proteochemometric modeling in a Bayesian framework. PMID:25045403
How proteins bind macrocycles. PMID:25038790
Analysis of the protein domain and domain architecture content in fungi and its application in the search of new antifungal targets. PMID:25033262
Asymmetric clustering index in a case study of 5-HT1A receptor ligands. PMID:25019251
Design of an activity landscape view taking compound-based feature probabilities into account. PMID:25001923
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion. PMID:24976868
The influence of negative training set size on machine learning-based virtual screening. PMID:24976867
Industrial applications of in silico ADMET. PMID:24972798
Elucidating polypharmacological mechanisms of polyphenols by gene module profile analysis. PMID:24968267
Profiling animal toxicants by automatically mining public bioassay data: a big data approach for computational toxicology. PMID:24950175
IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PMID:24949626
Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. PMID:24936211
In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. PMID:24928891
Exploring the chemical space of multitarget ligands using aligned self-organizing maps. PMID:24900624
Chemical Probe Identification Platform for Orphan GPCRs Using Focused Compound Screening: GPR39 as a Case Example. PMID:24900608
Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics. PMID:24884876
SuperPred: update on drug classification and target prediction. PMID:24878925
Expanding the fragrance chemical space for virtual screening. PMID:24876890
Many approved drugs have bioactive analogs with different target annotations. PMID:24871342
Novel design strategy for checkpoint kinase 2 inhibitors using pharmacophore modeling, combinatorial fusion, and virtual screening. PMID:24864236
Molecular modelling study of the PPARγ receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis. PMID:24857909
DINIES: drug-target interaction network inference engine based on supervised analysis. PMID:24838565
Towards structural systems pharmacology to study complex diseases and personalized medicine. PMID:24830652
Predicting mTOR inhibitors with a classifier using recursive partitioning and Naïve Bayesian approaches. PMID:24819222
An atlas of genetic influences on human blood metabolites. PMID:24816252
Activation and repression of Epstein-Barr Virus and Kaposi's sarcoma-associated herpesvirus lytic cycles by short- and medium-chain fatty acids. PMID:24807711
Tuning HERG out: antitarget QSAR models for drug development. PMID:24805060
Computational chemogenomics: is it more than inductive transfer? PMID:24771144
Targeting bromodomains: epigenetic readers of lysine acetylation. PMID:24751816
Model for vaccine design by prediction of B-epitopes of IEDB given perturbations in peptide sequence, in vivo process, experimental techniques, and source or host organisms. PMID:24741624
Advancing the activity cliff concept, part II. PMID:24741442
TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. PMID:24735618
Label-free drug discovery. PMID:24723889
Toward more realistic drug-target interaction predictions. PMID:24723570
Chemical, target, and bioactive properties of allosteric modulation. PMID:24699297
Applying a multitarget rational drug design strategy: the first set of modulators with potent and balanced activity toward dopamine D3 receptor and fatty acid amide hydrolase. PMID:24691497
Exploring compound promiscuity patterns and multi-target activity spaces. PMID:24688751
Hybrid integrated label-free chemical and biological sensors. PMID:24675757
Molpher: a software framework for systematic chemical space exploration. PMID:24655571
Linking off-target kinase pharmacology to the differential cellular effects observed among PARP inhibitors. PMID:24632590
Drug2Gene: an exhaustive resource to explore effectively the drug-target relation network. PMID:24618344
Thematic series on biomedical ontologies in JBMS: challenges and new directions. PMID:24602198
Using matched molecular series as a predictive tool to optimize biological activity. PMID:24601597
Discovery of potent positive allosteric modulators of the α3β2 nicotinic acetylcholine receptor by a chemical space walk in ChEMBL. PMID:24593915
Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands. PMID:24567719
Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets. PMID:24565165
Pathway-based drug repositioning using causal inference. PMID:24564553
Advancing the activity cliff concept. PMID:24555097
In silico prediction of antimalarial drug target candidates. PMID:24533280
Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database. PMID:24533037
Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells. PMID:24530226
QSAR modeling of imbalanced high-throughput screening data in PubChem. PMID:24524735
Identification of novel serotonin transporter compounds by virtual screening. PMID:24521202
SAMPL4 & DOCK3.7: lessons for automated docking procedures. PMID:24515818
PFClust: an optimised implementation of a parameter-free clustering algorithm. PMID:24490618
Efficient ring perception for the Chemistry Development Kit. PMID:24479757
Formation of activity cliffs is accompanied by systematic increases in ligand efficiency from lowly to highly potent compounds. PMID:24477941
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. PMID:24470572
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. PMID:24441647
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Amyloid-precursor-protein-lowering small molecules for disease modifying therapy of Alzheimer's disease. PMID:24367508
Web search and data mining of natural products and their bioactivities in PubChem. PMID:24363665
Substrate sequences tell similar stories as binding cavities: commentary. PMID:24359119
Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications. PMID:24358818
LigSearch: a knowledge-based web server to identify likely ligands for a protein target. PMID:24311580
BacMet: antibacterial biocide and metal resistance genes database. PMID:24304895
canSAR: updated cancer research and drug discovery knowledgebase. PMID:24304894
Prediction of off-target drug effects through data fusion. PMID:24297543
Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. PMID:24297541
Challenges in secondary analysis of high throughput screening data. PMID:24297539
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Seeding collaborations to advance kinase science with the GSK Published Kinase Inhibitor Set (PKIS). PMID:24283969
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. PMID:24283849
Predicting drug-target interactions using drug-drug interactions. PMID:24278248
PAV ontology: provenance, authoring and versioning. PMID:24267948
myChEMBL: a virtual machine implementation of open data and cheminformatics tools. PMID:24262214
Development of a decision tree to classify the most accurate tissue-specific tissue to plasma partition coefficient algorithm for a given compound. PMID:24258064
Substrate-driven mapping of the degradome by comparison of sequence logos. PMID:24244149
FireDB: a compendium of biological and pharmacologically relevant ligands. PMID:24243844
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
The ChEMBL bioactivity database: an update. PMID:24214965
Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes. PMID:24210220
Tracking 20 years of compound-to-target output from literature and patents. PMID:24204758
A comprehensive survey of small-molecule binding pockets in proteins. PMID:24204237
DrugBank 4.0: shedding new light on drug metabolism. PMID:24203711
PubChem BioAssay: 2014 update. PMID:24198245
Prediction of the P. falciparum target space relevant to malaria drug discovery. PMID:24146604
Pathways of Toxicity. PMID:24127042
The importance of molecular complexity in the design of screening libraries. PMID:24122490
DGIdb: mining the druggable genome. PMID:24122041
Antibacterial mechanisms identified through structural systems pharmacology. PMID:24112686
Ligand pose and orientational sampling in molecular docking. PMID:24098414
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PMID:24098102
Selective anticancer agents suppress aging in Drosophila. PMID:24096697
Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs). PMID:24088245
Identification of new natural DNA G-quadruplex binders selected by a structure-based virtual screening approach. PMID:24084014
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways. PMID:24068907
Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods. PMID:24063533
K-Map: connecting kinases with therapeutics for drug repurposing and development. PMID:24060470
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. PMID:24059743
Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors. PMID:24021214
Using molecular features of xenobiotics to predict hepatic gene expression response. PMID:24010729
Computational models for neglected diseases: gaps and opportunities. PMID:23990313
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Systematic mining of analog series with related core structures in multi-target activity space. PMID:23975272
Chemically Advanced Template Search (CATS) for Scaffold-Hopping and Prospective Target Prediction for 'Orphan' Molecules. PMID:23956801
Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors. PMID:23936032
Linking Ayurveda and Western medicine by integrative analysis. PMID:23930045
Check your confidence: size really does matter. PMID:23909878
Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. PMID:23887926
MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways. PMID:23875173
CREDO: a structural interactomics database for drug discovery. PMID:23868908
Bioinformatic screening of autoimmune disease genes and protein structure prediction with FAMS for drug discovery. PMID:23855671
Model for high-throughput screening of multitarget drugs in chemical neurosciences: synthesis, assay, and theoretic study of rasagiline carbamates. PMID:23855599
Inferring multi-target QSAR models with taxonomy-based multi-task learning. PMID:23842210
Predicting drug-target interactions using restricted Boltzmann machines. PMID:23812976
Protein pocket and ligand shape comparison and its application in virtual screening. PMID:23807262
Predicting the protein targets for athletic performance-enhancing substances. PMID:23800040
The open access malaria box: a drug discovery catalyst for neglected diseases. PMID:23798988
The CARLSBAD database: a confederated database of chemical bioactivities. PMID:23794735
TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. PMID:23766369
Drug repurposing: mining protozoan proteomes for targets of known bioactive compounds. PMID:23757409
Open-source platform to benchmark fingerprints for ligand-based virtual screening. PMID:23721588
A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design. PMID:23713847
Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches. PMID:23707773
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PMID:23704901
Interplay of physics and evolution in the likely origin of protein biochemical function. PMID:23690621
A semi-supervised method for drug-target interaction prediction with consistency in networks. PMID:23667553
The ChEMBL database as linked open data. PMID:23657106
Use of natural products as chemical library for drug discovery and network pharmacology. PMID:23638153
Systematic identification of proteins that elicit drug side effects. PMID:23632385
Extracting and connecting chemical structures from text sources using chemicalize.org. PMID:23618056
CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. PMID:23617227
Comparability of mixed IC₅₀ data - a statistical analysis. PMID:23613770
Toward a general predictive QSAR model for gamma-secretase inhibitors. PMID:23612850
What is the likelihood of an active compound to be promiscuous? Systematic assessment of compound promiscuity on the basis of PubChem confirmatory bioassay data. PMID:23605807
Discovery of the inhibitory effect of a phosphatidylinositol derivative on P-glycoprotein by virtual screening followed by in vitro cellular studies. PMID:23593281
Genome-scale screening of drug-target associations relevant to Ki using a chemogenomics approach. PMID:23577055
PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery. PMID:23548981
De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments. PMID:23534475
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics. PMID:23514033
Profile of the GSK published protein kinase inhibitor set across ATP-dependent and-independent luciferases: implications for reporter-gene assays. PMID:23505445
Brain: biomedical knowledge manipulation. PMID:23505292
Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. PMID:23485065
Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). PMID:23473803
The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. PMID:23473072
Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases. PMID:23447100
Colloidal aggregation causes inhibition of G protein-coupled receptors. PMID:23437772
Informatics confronts drug-drug interactions. PMID:23414686
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. PMID:23409953
Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PMID:23408876
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Drug repurposing screen reveals FDA-approved inhibitors of human HMG-CoA reductase and isoprenoid synthesis that block Cryptosporidium parvum growth. PMID:23380723
Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance. PMID:23361103
A ligand's-eye view of protein similarity. PMID:23361090
Target deconvolution techniques in modern phenotypic profiling. PMID:23337810
UniChem: a unified chemical structure cross-referencing and identifier tracking system. PMID:23317286
SARConnect: A Tool to Interrogate the Connectivity Between Proteins, Chemical Structures and Activity Data. PMID:23308082
Activity cliffs in PubChem confirmatory bioassays taking inactive compounds into account. PMID:23296990
Annotating Human P-Glycoprotein Bioassay Data. PMID:23293680
The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space. PMID:23293679
TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database. PMID:23292636
A pharmacological organization of G protein-coupled receptors. PMID:23291723
Mapping small molecule binding data to structural domains. PMID:23282026
Objective assessment of cancer genes for drug discovery. PMID:23274470
Polypharmacology: drug discovery for the future. PMID:23272792
FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. PMID:23240691
Consistency of systematic chemical identifiers within and between small-molecule databases. PMID:23237381
Automated design of ligands to polypharmacological profiles. PMID:23235874
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
Limits of ligand selectivity from docking to models: in silico screening for A(1) adenosine receptor antagonists. PMID:23185482
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
The chemical interactome space between the human host and the genetically defined gut metabotypes. PMID:23178670
The EBI enzyme portal. PMID:23175605
SwissBioisostere: a database of molecular replacements for ligand design. PMID:23161688
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints. PMID:23131020
Enzyme informatics. PMID:23116471
How promiscuous are pharmaceutically relevant compounds? A data-driven assessment. PMID:23090085
Computational tools and resources for metabolism-related property predictions. 1. Overview of publicly available (free and commercial) databases and software. PMID:23088273
IUPHAR-DB: updated database content and new features. PMID:23087376
IADE: a system for intelligent automatic design of bioisosteric analogs. PMID:23053736
Exploring chemical space for drug discovery using the chemical universe database. PMID:23019491
Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI. PMID:22989151
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Extraction and validation of substructure profiles for enriching compound libraries. PMID:22983491
Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening. PMID:22972561
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader. PMID:22947092
Assessing drug target association using semantic linked data. PMID:22859915
Rationalizing structure and target relationships between current drugs. PMID:22826035
Prediction of chemical-protein interactions network with weighted network-based inference method. PMID:22815915
AtlasCBS: a web server to map and explore chemico-biological space. PMID:22798082
The Molecule Cloud - compact visualization of large collections of molecules. PMID:22769057
HEMD: an integrated tool of human epigenetic enzymes and chemical modulators for therapeutics. PMID:22761927
Public domain databases for medicinal chemistry. PMID:22731701
Large-scale prediction and testing of drug activity on side-effect targets. PMID:22722194
Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. PMID:22716043
Identifying mechanism-of-action targets for drugs and probes. PMID:22711801
Natural product-likeness score revisited: an open-source, open-data implementation. PMID:22607271
ZINC: a free tool to discover chemistry for biology. PMID:22587354
Determination of minimal transcriptional signatures of compounds for target prediction. PMID:22574917
FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. PMID:22574683
Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets. PMID:22434711
Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4. PMID:22431600
Global phenotypic screening for antimalarials. PMID:22284359
KB-Rank: efficient protein structure and functional annotation identification via text query. PMID:22270457
PubChem's BioAssay Database. PMID:22140110
MetaBase--the wiki-database of biological databases. PMID:22139927
TDR Targets: a chemogenomics resource for neglected diseases. PMID:22116064
PDBe: Protein Data Bank in Europe. PMID:22110033
STITCH 3: zooming in on protein-chemical interactions. PMID:22075997
SuperTarget goes quantitative: update on drug-target interactions. PMID:22067455
Classification of scaffold-hopping approaches. PMID:22056715
canSAR: an integrated cancer public translational research and drug discovery resource. PMID:22013161
The ChEMBL database in 2017 PubMed citations: 558.

558 articles citing: The ChEMBL database in 2017

Repurposing of a human antibody-based microarray to explore conserved components of the signalome of the parasitic nematode Haemonchus contortus. PMID:35907892
Confidence bands and hypothesis tests for hit enrichment curves. PMID:35902962
QSAR Evaluations to Unravel the Structural Features in Lysine-Specific Histone Demethylase 1A Inhibitors for Novel Anticancer Lead Development Supported by Molecular Docking, MD Simulation and MMGBSA. PMID:35897936
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Maximizing the Performance of Similarity-Based Virtual Screening Methods by Generating Synergy from the Integration of 2D and 3D Approaches. PMID:35887097
Subtype of Neuroblastoma Cells with High KIT Expression Are Dependent on KIT and Its Knockdown Induces Compensatory Activation of Pro-Survival Signaling. PMID:35887076
Identification of New Toxicity Mechanisms in Drug-Induced Liver Injury through Systems Pharmacology. PMID:35886075
SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. PMID:35873673
Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library. PMID:35873314
Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules. PMID:35860225
A transfer learning approach for reaction discovery in small data situations using generative model. PMID:35832891
SARS-CoV-2 potential drugs, drug targets, and biomarkers: a viral-host interaction network-based analysis. PMID:35831333
Machine Learning for Discovery of New ADORA Modulators. PMID:35814244
Most Pathways Can Be Related to the Pathogenesis of Alzheimer's Disease. PMID:35813951
Identification of potent aldose reductase inhibitors as antidiabetic (Anti-hyperglycemic) agents using QSAR based virtual Screening, molecular Docking, MD simulation and MMGBSA approaches. PMID:35812153
Identifying Lethal Dependencies with HUGE Predictive Power. PMID:35805023
Mechanism assay of interaction between blood vessels-near infrared probe and cell surface marker proteins of endothelial cells. PMID:35795137
Toward in Silico Modeling of Dynamic Combinatorial Libraries. PMID:35756377
Memory augmented recurrent neural networks for de-novo drug design. PMID:35737661
Using BERT to identify drug-target interactions from whole PubMed. PMID:35729494
MegaSyn: Integrating Generative Molecular Design, Automated Analog Designer, and Synthetic Viability Prediction. PMID:35694522
Molecular Similarity Perception Based on Machine-Learning Models. PMID:35682792
Investigation of the mechanism of Shen Qi Wan prescription in the treatment of T2DM via network pharmacology and molecular docking. PMID:35673584
Drug Design by Pharmacophore and Virtual Screening Approach. PMID:35631472
An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway. PMID:35625318
Machine Learning in Antibacterial Drug Design. PMID:35592425
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA. PMID:35581483
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. PMID:35579568
Endophenotype-based in silico network medicine discovery combined with insurance record data mining identifies sildenafil as a candidate drug for Alzheimer's disease. PMID:35572351
Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites. PMID:35563976
Visualization of Topological Pharmacophore Space with Graph Edit Distance. PMID:35559135
Exploring the chemical space and the bioactivity profile of lactams: a chemoinformatic study. PMID:35528563
Ligand discrimination during virtual screening of the CB1 cannabinoid receptor crystal structures following cross-docking and microsecond molecular dynamics simulations. PMID:35521393
Chemical space exploration guided by deep neural networks. PMID:35514634
FAME: Fragment-based Conditional Molecular Generation for Phenotypic Drug Discovery. PMID:35509686
Structurally diverse diterpenoid alkaloids from the lateral roots of Aconitum carmichaelii Debx. and their anti-tumor activities based on in vitro systematic evaluation and network pharmacology analysis. PMID:35480028
Δ-Quantum machine-learning for medicinal chemistry. PMID:35470831
Bipartite network models to design combination therapies in acute myeloid leukaemia. PMID:35440130
Predicting hERG channel blockers with directed message passing neural networks. PMID:35425351
Synthesis of potent and selective HDAC6 inhibitors led to unexpected opening of a quinazoline ring. PMID:35425078
Pulmonary Inflammatory Response in Lethal COVID-19 Reveals Potential Therapeutic Targets and Drugs in Phases III/IV Clinical Trials. PMID:35422702
Accurate prediction of molecular targets using a self-supervised image representation learning framework. PMID:35411337
Predicting the binding of small molecules to nuclear receptors using machine learning. PMID:35383362
AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials. PMID:35365662
Computational Repurposing of Drugs and Natural Products Against SARS-CoV-2 Main Protease (Mpro) as Potential COVID-19 Therapies. PMID:35359601
Relationship between Hormonal Modulation and Gastroprotective Activity of Malvidin and Cyanidin Chloride: In Vivo and In Silico Approach. PMID:35335941
Prediction of the Neurotoxic Potential of Chemicals Based on Modelling of Molecular Initiating Events Upstream of the Adverse Outcome Pathways of (Developmental) Neurotoxicity. PMID:35328472
Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. PMID:35323700
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Machine learning prediction of 3CLpro SARS-CoV-2 docking scores. PMID:35288359
Chemogenomic Approaches for Revealing Drug Target Interactions in Drug Discovery. PMID:35283667
Retrosynthetic reaction pathway prediction through neural machine translation of atomic environments. PMID:35246540
Design of SARS-CoV-2 Mpro, PLpro dual-target inhibitors based on deep reinforcement learning and virtual screening. PMID:35220726
Discovery of Kinase and Carbonic Anhydrase Dual Inhibitors by Machine Learning Classification and Experiments. PMID:35215348
wSDTNBI: a novel network-based inference method for virtual screening. PMID:35211272
Human-Based Immune Responsive In Vitro Infection Models for Validation of Novel TLR4 Antagonists Identified by Computational Discovery. PMID:35208698
Hydroxamic Acid as a Potent Metal-Binding Group for Inhibiting Tyrosinase. PMID:35204163
Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations. PMID:35203788
Identification of Dysregulated Expression of G Protein Coupled Receptors in Endocrine Tumors by Bioinformatics Analysis: Potential Drug Targets? PMID:35203352
Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor. PMID:35195401
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models. PMID:35191696
Development of In Silico Methods for Toxicity Prediction in Collaboration Between Academia and the Pharmaceutical Industry. PMID:35188630
Patient-specific Boolean models of signalling networks guide personalised treatments. PMID:35164900
DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design. PMID:35163948
A platform for oncogenomic reporting and interpretation. PMID:35140225
A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. PMID:35106508
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. PMID:35081108
Mycobacterium abscessus drug discovery using machine learning. PMID:35077930
Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels. PMID:35071887
Allosteric modulation of dopamine D2L receptor in complex with Gi1 and Gi2 proteins: the effect of subtle structural and stereochemical ligand modifications. PMID:35064921
The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience. PMID:35054998
Molecular docking-based computational platform for high-throughput virtual screening. PMID:35039800
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins. PMID:35020376
Evaluation of Virtual Screening Strategies for the Identification of γ-Secretase Inhibitors and Modulators. PMID:35011410
Commercial SARS-CoV-2 Targeted, Protease Inhibitor Focused and Protein-Protein Interaction Inhibitor Focused Molecular Libraries for Virtual Screening and Drug Design. PMID:35008818
A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study. PMID:35001230
Amelioration of Alzheimer's disease pathology by mitophagy inducers identified via machine learning and a cross-species workflow. PMID:34992270
Structure-Based Drug Discovery of IRE1 Modulators. PMID:34985708
In Silico Prediction and Bioactivity Evaluation of Chemical Ingredients Against Influenza A Virus From Isatis tinctoria L. PMID:34950027
Drug Discovery for Mycobacterium tuberculosis Using Structure-Based Computer-Aided Drug Design Approach. PMID:34948055
Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. PMID:34946572
Set-Theoretic Formalism for Treating Ligand-Target Datasets. PMID:34946500
Identifying diverse metal oxide nanomaterials with lethal effects on embryonic zebrafish using machine learning. PMID:34934606
Sdfconf: A Novel, Flexible, and Robust Molecular Data Management Tool. PMID:34932340
Transformer-Based Generative Model Accelerating the Development of Novel BRAF Inhibitors. PMID:34926933
Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes. PMID:34921117
Social Isolation: How Can the Effects on the Cholinergic System Be Isolated? PMID:34916930
Wet-dry-wet drug screen leads to the synthesis of TS1, a novel compound reversing lung fibrosis through inhibition of myofibroblast differentiation. PMID:34916483
Structural systems pharmacology: A framework for integrating metabolic network and structure-based virtual screening for drug discovery against bacteria. PMID:34905555
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Splitting chemical structure data sets for federated privacy-preserving machine learning. PMID:34876230
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology. PMID:34873596
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis. PMID:34850112
Transformational machine learning: Learning how to learn from many related scientific problems. PMID:34845013
Mapping Compound Databases to Disease Maps-A MINERVA Plugin for CandActBase. PMID:34834423
Data-Driven Analysis of Fluorination of Ligands of Aminergic G Protein Coupled Receptors. PMID:34827645
Development of a chemogenomics library for phenotypic screening. PMID:34819133
Fine tuning for success in structure-based virtual screening. PMID:34799816
Effective Search of Triterpenes with Anti-HSV-1 Activity Using a Classification Model by Logistic Regression. PMID:34796164
DockStream: a docking wrapper to enhance de novo molecular design. PMID:34789335
Chagas Disease Drug Discovery in Latin America-A Mini Review of Antiparasitic Agents Explored Between 2010 and 2021. PMID:34778217
Molecular generation by Fast Assembly of (Deep)SMILES fragments. PMID:34775976
Prediction of Anti-Glioblastoma Drug-Decorated Nanoparticle Delivery Systems Using Molecular Descriptors and Machine Learning. PMID:34768951
Img2Mol - accurate SMILES recognition from molecular graphical depictions. PMID:34760202
Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. PMID:34745807
Explainable machine learning predictions of dual-target compounds reveal characteristic structural features. PMID:34732806
Has Artificial Intelligence Impacted Drug Discovery? PMID:34731468
An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci. PMID:34711957
Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. PMID:34705221
Searchable database of frequent R-groups in medicinal chemistry and their preferred replacements. PMID:34692956
In Silico Identification of Possible Inhibitors for Protein Kinase B (PknB) of Mycobacterium tuberculosis. PMID:34684743
Screening of β1- and β2-Adrenergic Receptor Modulators through Advanced Pharmacoinformatics and Machine Learning Approaches. PMID:34681845
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. PMID:34676613
Pseudonatural Products Occur Frequently in Biologically Relevant Compounds. PMID:34669418
Unravelling the collateral damage of antibiotics on gut bacteria. PMID:34646011
Multi-instance learning of graph neural networks for aqueous pKa prediction. PMID:34643666
Individual and collective human intelligence in drug design: evaluating the search strategy. PMID:34635158
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors. PMID:34622387
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation. PMID:34600580
A Network Pharmacology Study on the Molecular Mechanism of Protocatechualdehyde in the Treatment of Diabetic Cataract. PMID:34594100
COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19. PMID:34593915
Computational Prediction of Chemical Tools for Identification and Validation of Synthetic Lethal Interaction Networks. PMID:34590285
Polypharmacology of clinical sodium glucose co-transport protein 2 inhibitors and relationship to suspected adverse drug reactions. PMID:34586753
Inhibitors of histone deacetylase 6 based on a novel 3-hydroxy-isoxazole zinc binding group. PMID:34583596
Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma. PMID:34577052
Comprehensive Survey of Recent Drug Discovery Using Deep Learning. PMID:34576146
Inhibition of Class A β-Lactamase (TEM-1) by Narrow Fractions of Humic Substances. PMID:34568667
Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery. PMID:34554348
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning. PMID:34551818
Network-Based Identification and Experimental Validation of Drug Candidates Toward SARS-CoV-2 via Targeting Virus-Host Interactome. PMID:34539756
Deep learning identifies synergistic drug combinations for treating COVID-19. PMID:34526388
Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications. PMID:34500724
Computational Prediction of Compound-Protein Interactions for Orphan Targets Using CGBVS. PMID:34500569
Machine learning methods, databases and tools for drug combination prediction. PMID:34477201
Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. PMID:34472587
Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking. PMID:34469692
Selective DNA Gyrase Inhibitors: Multi-Target in Silico Profiling with 3D-Pharmacophores. PMID:34451886
Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer. PMID:34450249
Deciphering osteoarthritis genetics across 826,690 individuals from 9 populations. PMID:34450027
An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. PMID:34447313
Chemoinformatics Analyses of Tau Ligands Reveal Key Molecular Requirements for the Identification of Potential Drug Candidates against Tauopathies. PMID:34443629
Design of Multifaceted Antioxidants: Shifting towards Anti-Inflammatory and Antihyperlipidemic Activity. PMID:34443516
Identification of Broad-Spectrum MMP Inhibitors by Virtual Screening. PMID:34361703
BonMOLière: Small-Sized Libraries of Readily Purchasable Compounds, Optimized to Produce Genuine Hits in Biological Screens across the Protein Space. PMID:34360558
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
Plasma proteins, cognitive decline, and 20-year risk of dementia in the Whitehall II and Atherosclerosis Risk in Communities studies. PMID:34338426
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool. PMID:34301327
Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus. PMID:34286575
ERpred: a web server for the prediction of subtype-specific estrogen receptor antagonists. PMID:34285834
Norepinephrine Protects against Methamphetamine Toxicity through β2-Adrenergic Receptors Promoting LC3 Compartmentalization. PMID:34281286
Mycobacterium tuberculosis Cell Wall Permeability Model Generation Using Chemoinformatics and Machine Learning Approaches. PMID:34278133
TITAN: T-cell receptor specificity prediction with bimodal attention networks. PMID:34252922
The Application of In Silico Methods on Umami Taste Receptor. PMID:34247277
Feature importance correlation from machine learning indicates functional relationships between proteins and similar compound binding characteristics. PMID:34244588
Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay. PMID:34234012
Curated Data In - Trustworthy In Silico Models Out: The Impact of Data Quality on the Reliability of Artificial Intelligence Models as Alternatives to Animal Testing. PMID:34233495
Nonadditivity in public and inhouse data: implications for drug design. PMID:34215341
Predicting Drug-Target Interactions Based on the Ensemble Models of Multiple Feature Pairs. PMID:34202954
Antiviral Activity of Metabolites from Peruvian Plants against SARS-CoV-2: An In Silico Approach. PMID:34202092
Elucidating the Mechanism of Action of the Attributed Immunomodulatory Role of Eltrombopag in Primary Immune Thrombocytopenia: An In Silico Approach. PMID:34199099
Learning from Nature: From a Marine Natural Product to Synthetic Cyclooxygenase-1 Inhibitors by Automated De Novo Design. PMID:34176236
Retrosynthetic accessibility score (RAscore) - rapid machine learned synthesizability classification from AI driven retrosynthetic planning. PMID:34164104
Scaffold fragmentation and substructure hopping reveal potential, robustness, and limits of computer-aided pattern analysis (C@PA). PMID:34141145
Active Learning and the Potential of Neural Networks Accelerate Molecular Screening for the Design of a New Molecule Effective against SARS-CoV-2. PMID:34124259
Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES. PMID:34123336
Algebraic graph-assisted bidirectional transformers for molecular property prediction. PMID:34112777
Neuraldecipher - reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures. PMID:34094299
Siamese Recurrent Neural Network with a Self-Attention Mechanism for Bioactivity Prediction. PMID:34056263
Fine-tuning of a generative neural network for designing multi-target compounds. PMID:34046745
Masked graph modeling for molecule generation. PMID:34039973
Quantum Machine Learning Algorithms for Drug Discovery Applications. PMID:34032436
LigAdvisor: a versatile and user-friendly web-platform for drug design. PMID:34023895
Evaluation of Quantitative Structure Property Relationship Algorithms for Predicting Plasma Protein Binding in Humans. PMID:34017929
Common genetic associations between age-related diseases. PMID:33959723
Uncovering genetic mechanisms of hypertension through multi-omic analysis of the kidney. PMID:33958779
Elucidating direct kinase targets of compound Danshen dropping pills employing archived data and prediction models. PMID:33953309
Methods for Molecular Modelling of Protein Complexes. PMID:33950384
GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds. PMID:33947911
Evaluating Alternatives to Water as Solvents for Life: The Example of Sulfuric Acid. PMID:33925658
Antifungal Activity and DNA Topoisomerase Inhibition of Hydrolysable Tannins from Punica granatum L. PMID:33920681
Ligand-Receptor Interactions and Machine Learning in GCGR and GLP-1R Drug Discovery. PMID:33920024
Cluster Analysis of Medicinal Plants and Targets Based on Multipartite Network. PMID:33917905
Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology. PMID:33904641
Flame: an open source framework for model development, hosting, and usage in production environments. PMID:33875019
Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors. PMID:33856768
Machine learning reveals that structural features distinguishing promiscuous and non-promiscuous compounds depend on target combinations. PMID:33846469
A review on compound-protein interaction prediction methods: Data, format, representation and model. PMID:33841755
Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. PMID:33806075
Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein-protein interaction-oriented library and machine learning. PMID:33795749
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction. PMID:33758923
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Prediction of activity cliffs on the basis of images using convolutional neural networks. PMID:33740200
In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19. PMID:33716737
Drug Repurposing and Polypharmacology to Fight SARS-CoV-2 Through Inhibition of the Main Protease. PMID:33692695
Association of Antihypertensive Drug Target Genes With Psychiatric Disorders: A Mendelian Randomization Study. PMID:33688928
Profiling the structural determinants of aminoketone derivatives as hNET and hDAT reuptake inhibitors by field-based QSAR based on molecular docking. PMID:33682763
PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds. PMID:33672700
Mechanistic Insights into Side Effects of Troglitazone and Rosiglitazone Using a Novel Inverse Molecular Docking Protocol. PMID:33670968
Network Analysis Identifies Drug Targets and Small Molecules to Modulate Apoptosis Resistant Cancers. PMID:33670487
Novel Development of Predictive Feature Fingerprints to Identify Chemistry-Based Features for the Effective Drug Design of SARS-CoV-2 Target Antagonists and Inhibitors Using Machine Learning. PMID:33644594
Rational design of potent anti-COVID-19 main protease drugs: An extensive multi-spectrum in silico approach. PMID:33612899
Identification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening. PMID:33612076
Data set of competitive and allosteric protein kinase inhibitors confirmed by X-ray crystallography. PMID:33604432
Machine learning identifies candidates for drug repurposing in Alzheimer's disease. PMID:33589615
Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities. PMID:33588902
Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates. PMID:33577681
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations. PMID:33577560
Advances in de Novo Drug Design: From Conventional to Machine Learning Methods. PMID:33562347
In silico identification of natural products from Traditional Chinese Medicine for cancer immunotherapy. PMID:33558586
Using Bibliometric Analysis and Machine Learning to Identify Compounds Binding to Sialidase-1. PMID:33553934
Generative chemistry: drug discovery with deep learning generative models. PMID:33543405
Evaluating Deep Learning models for predicting ALK-5 inhibition. PMID:33508008
Machine learning applications in drug development. PMID:33489002
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
Enabling High-Throughput Searches for Multiple Chemical Data Using the U.S.-EPA CompTox Chemicals Dashboard. PMID:33481596
Pyrazolyl-pyrimidones inhibit the function of human solute carrier protein SLC11A2 (hDMT1) by metal chelation. PMID:33479694
Introducing a new category of activity cliffs combining different compound similarity criteria. PMID:33479613
An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease. PMID:33466870
Evaluating and evolving a screening library in academia: the St Jude approach. PMID:33453364
Homobivalent Lamellarin-Like Schiff Bases: In Vitro Evaluation of Their Cancer Cell Cytotoxicity and Multitargeting Anti-Alzheimer's Disease Potential. PMID:33445600
Compressed graph representation for scalable molecular graph generation. PMID:33431050
EvoMol: a flexible and interpretable evolutionary algorithm for unbiased de novo molecular generation. PMID:33431049
Visualization of very large high-dimensional data sets as minimum spanning trees. PMID:33431043
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. PMID:33431036
The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. PMID:33431029
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
SMILES-based deep generative scaffold decorator for de-novo drug design. PMID:33431013
Review on natural products databases: where to find data in 2020. PMID:33431011
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. PMID:33431010
Mol-CycleGAN: a generative model for molecular optimization. PMID:33431006
Activity landscape image analysis using convolutional neural networks. PMID:33431003
Craig plot 2.0: an interactive navigation in the substituent bioisosteric space. PMID:33431001
GEN: highly efficient SMILES explorer using autodidactic generative examination networks. PMID:33430998
A visual approach for analysis and inference of molecular activity spaces. PMID:33430986
Efficient learning of non-autoregressive graph variational autoencoders for molecular graph generation. PMID:33430985
Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors. PMID:33430983
The chemfp project. PMID:33430977
A general approach for retrosynthetic molecular core analysis. PMID:33430974
Randomized SMILES strings improve the quality of molecular generative models. PMID:33430971
Industry-scale application and evaluation of deep learning for drug target prediction. PMID:33430964
A de novo molecular generation method using latent vector based generative adversarial network. PMID:33430938
Hierarchical Graph Representation of Pharmacophore Models. PMID:33425991
COCONUT online: Collection of Open Natural Products database. PMID:33423696
Profiling and analysis of chemical compounds using pointwise mutual information. PMID:33423694
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Artificial Intelligence-Based Application to Explore Inhibitors of Neurodegenerative Diseases. PMID:33414713
A review of optical chemical structure recognition tools. PMID:33372625
Image-based profiling for drug discovery: due for a machine-learning upgrade? PMID:33353986
Bioactivity Comparison across Multiple Machine Learning Algorithms Using over 5000 Datasets for Drug Discovery. PMID:33325717
Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. PMID:33322692
Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? PMID:33322568
A Computer-Aided Drug Design Approach to Predict Marine Drug-Like Leads for SARS-CoV-2 Main Protease Inhibition. PMID:33322052
Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy. PMID:33312959
Repurposing Known Drugs as Covalent and Non-covalent Inhibitors of the SARS-CoV-2 Papain-Like Protease. PMID:33304884
Minimal information for Chemosensitivity assays (MICHA): A next-generation pipeline to enable the FAIRification of drug screening experiments. PMID:33300000
Memory-assisted reinforcement learning for diverse molecular de novo design. PMID:33292554
Repurposing of FDA approved ring systems through bi-directional target-ring system dual screening. PMID:33273509
Acylpolyamine Mygalin as a TLR4 Antagonist Based on Molecular Docking and In Vitro Analyses. PMID:33271940
A Multi-Objective Approach for Anti-Osteosarcoma Cancer Agents Discovery through Drug Repurposing. PMID:33266378
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:33219674
PROMISCUOUS 2.0: a resource for drug-repositioning. PMID:33196798
Repurposed drugs and nutraceuticals targeting envelope protein: A possible therapeutic strategy against COVID-19. PMID:33189776
Pharmacology-informed prediction of the risk posed to fish by mixtures of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment. PMID:33157376
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
Prediction of Protein-ligand Interaction Based on Sequence Similarity and Ligand Structural Features. PMID:33142754
Perturbation-Theory Machine Learning (PTML) Multilabel Model of the ChEMBL Dataset of Preclinical Assays for Antisarcoma Compounds. PMID:33134682
Systems pharmacology approach uncovers Ligustilide attenuates experimental colitis in mice by inhibiting PPARγ-mediated inflammation pathways. PMID:33130971
Machine Learning for Discovery of GSK3β Inhibitors. PMID:33110983
Insights into the mechanism of Arnebia euchroma on leukemia via network pharmacology approach. PMID:33109189
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. PMID:33076254
signatureSearch: environment for gene expression signature searching and functional interpretation. PMID:33068417
Computational Approaches in Preclinical Studies on Drug Discovery and Development. PMID:33062633
SynPharm and the guide to pharmacology database: A toolset for conferring drug control on engineered proteins. PMID:33047381
In silico molecular target prediction unveils mebendazole as a potent MAPK14 inhibitor. PMID:33021050
SMARTS.plus - A Toolbox for Chemical Pattern Design. PMID:32997890
Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. PMID:32993084
Inhibitor bias in luciferase-based luminescence assays. PMID:32983562
Comprehensive assessment of side effects in COVID-19 drug pipeline from a network perspective. PMID:32971210
Systems pharmacology-based approach to investigate the mechanisms of Danggui-Shaoyao-san prescription for treatment of Alzheimer's disease. PMID:32948180
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. PMID:32931270
Kinase inhibitor data set for systematic analysis of representative kinases across the human kinome. PMID:32904416
Prediction of Promiscuity Cliffs Using Machine Learning. PMID:32881355
TargetDB: A target information aggregation tool and tractability predictor. PMID:32877430
Computational Method for Quantitative Comparison of Activity Landscapes on the Basis of Image Data. PMID:32872506
The COVID-19 Drug and Gene Set Library. PMID:32838343
Analysis on herbal medicines utilized for treatment of COVID-19. PMID:32834949
A unified view of density-based methods for semi-supervised clustering and classification. PMID:32831623
GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics. PMID:32786543
Predicting Drug-Target Interactions with Electrotopological State Fingerprints and Amphiphilic Pseudo Amino Acid Composition. PMID:32784497
Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. PMID:32779567
Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. PMID:32773989
Tales of 1,008 small molecules: phenomic profiling through live-cell imaging in a panel of reporter cell lines. PMID:32764586
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
The identification of dual protective agents against cisplatin-induced oto- and nephrotoxicity using the zebrafish model. PMID:32720645
Data Set Augmentation Allows Deep Learning-Based Virtual Screening to Better Generalize to Unseen Target Classes and Highlight Important Binding Interactions. PMID:32701288
Comparative Assessment of Protein Kinase Inhibitors in Public Databases and in PKIDB. PMID:32679723
An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models. PMID:32671093
Machine learning classification can reduce false positives in structure-based virtual screening. PMID:32669436
Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies. PMID:32664504
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
DrugSniper, a Tool to Exploit Loss-Of-Function Screens, Identifies CREBBP as a Predictive Biomarker of VOLASERTIB in Small Cell Lung Carcinoma (SCLC). PMID:32645997
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition. PMID:32645448
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). PMID:32566135
PhyteByte: identification of foods containing compounds with specific pharmacological properties. PMID:32522154
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. PMID:32511329
Scoring functions for drug-effect similarity. PMID:32484516
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
X-ray Structure-Based Chemoinformatic Analysis Identifies Promiscuous Ligands Binding to Proteins from Different Classes with Varying Shapes. PMID:32471121
Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. PMID:32440005
Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope. PMID:32438666
Chromenopyrimidinone Controls Stemness and Malignancy by suppressing CD133 Expression in Hepatocellular Carcinoma. PMID:32397206
Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. PMID:32381493
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands. PMID:32368908
Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders. PMID:32362822
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. PMID:32353859
TCMIO: A Comprehensive Database of Traditional Chinese Medicine on Immuno-Oncology. PMID:32351388
Predicting potential adverse events using safety data from marketed drugs. PMID:32349656
Parallel Generative Topographic Mapping: An Efficient Approach for Big Data Handling. PMID:32347666
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. PMID:32343143
In Silico Identification of Chemicals Capable of Binding to the Ecdysone Receptor. PMID:32335943
PyRod Enables Rational Homology Model-based Virtual Screening Against MCHR1. PMID:32329245
Multitarget Approach to Drug Candidates against Alzheimer's Disease Related to AChE, SERT, BACE1 and GSK3β Protein Targets. PMID:32316402
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Revealing cytotoxic substructures in molecules using deep learning. PMID:32297073
Structured reviews for data and knowledge-driven research. PMID:32283553
Novel Opioids: Systematic Web Crawling Within the e-Psychonauts' Scenario. PMID:32256304
Combining Virtual Screening Protocol and In Vitro Evaluation towards the Discovery of BACE1 Inhibitors. PMID:32244832
Computationally Empowered Workflow Identifies Novel Covalent Allosteric Binders for KRASG12C. PMID:32237114
Machine learning meets pK a. PMID:32226607
Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB). PMID:32213914
A Review on Applications of Computational Methods in Drug Screening and Design. PMID:32197324
Computational design of substrate selective inhibition. PMID:32196495
Deep Generative Models for 3D Linker Design. PMID:32195587
ccbmlib - a Python package for modeling Tanimoto similarity value distributions. PMID:32161645
Automated recognition of functional compound-protein relationships in literature. PMID:32126064
Structure-based discovery of potent and selective melatonin receptor agonists. PMID:32118583
ChEMBL-Likeness Score and Database GDBChEMBL. PMID:32117874
The e-Psychonauts' 'Spiced' World; Assessment of the Synthetic Cannabinoids' Information Available Online. PMID:32116194
Datasets and their influence on the development of computer assisted synthesis planning tools in the pharmaceutical domain. PMID:32110367
Using Machine Learning Methods and Structural Alerts for Prediction of Mitochondrial Toxicity. PMID:32108997
The kinase polypharmacology landscape of clinical PARP inhibitors. PMID:32066817
A systems approach to infectious disease. PMID:32060427
Biological Activity Profiles of Multitarget Ligands from X-ray Structures. PMID:32059498
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Functional group and diversity analysis of BIOFACQUIM: A Mexican natural product database. PMID:32047598
Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. PMID:32043883
Infection-based chemical screens uncover host-pathogen interactions. PMID:32036306
Is There a Role for Dual PI3K/mTOR Inhibitors for Patients Affected with Lymphoma? PMID:32033478
In Silico Strategies in Tuberculosis Drug Discovery. PMID:32033144
The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. PMID:32020584
SPVec: A Word2vec-Inspired Feature Representation Method for Drug-Target Interaction Prediction. PMID:31998687
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Discrimination of Naturally-Occurring 2-Arylbenzofurans as Cyclooxygenase-2 Inhibitors: Insights into the Binding Mode and Enzymatic Inhibitory Activity. PMID:31979339
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. PMID:31974851
A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules. PMID:31969612
Probabilistic Approach for Virtual Screening Based on Multiple Pharmacophores. PMID:31963467
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
Deciphering the enzymatic target of a new family of antischistosomal agents bearing a quinazoline scaffold using complementary computational tools. PMID:31939312
Combined network pharmacology and virtual reverse pharmacology approaches for identification of potential targets to treat vascular dementia. PMID:31937840
Machine and deep learning approaches for cancer drug repurposing. PMID:31904426
De novo generation of hit-like molecules from gene expression signatures using artificial intelligence. PMID:31900408
Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation. PMID:31894691
Indole-Containing Phytoalexin-Based Bioisosteres as Antifungals: In Vitro and In Silico Evaluation against Fusarium oxysporum. PMID:31877731
The human DEPhOsphorylation Database DEPOD: 2019 update. PMID:31836896
Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A. PMID:31814998
Search for Natural Compounds That Increase Apolipoprotein A-I Transcription in HepG2 Cells: Specific Attention for BRD4 Inhibitors. PMID:31814132
Deep learning of pharmacogenomics resources: moving towards precision oncology. PMID:31813953
A Bayesian graph convolutional network for reliable prediction of molecular properties with uncertainty quantification. PMID:31803423
Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. PMID:31803227
Validation Study of QSAR/DNN Models Using the Competition Datasets. PMID:31802634
Rethinking drug design in the artificial intelligence era. PMID:31801986
Current computational methods for predicting protein interactions of natural products. PMID:31762960
Identifying Promiscuous Compounds with Activity against Different Target Classes. PMID:31752252
Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research. PMID:31749705
Current developments in Coot for macromolecular model building of Electron Cryo-microscopy and Crystallographic Data. PMID:31730249
Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S. PMID:31729618
Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions. PMID:31724058
Mapping the perturbome network of cellular perturbations. PMID:31723137
Identification of Three Antimicrobials Activating Serotonin Receptor 4 in Colon Cells. PMID:31714751
In-Silico Molecular Binding Prediction for Human Drug Targets Using Deep Neural Multi-Task Learning. PMID:31703452
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. PMID:31701147
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
PDBe: improved findability of macromolecular structure data in the PDB. PMID:31691821
Norine: update of the nonribosomal peptide resource. PMID:31691799
Structure activity relationship studies on Amb639752: toward the identification of a common pharmacophoric structure for DGKα inhibitors. PMID:31690133
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
FoldamerDB: a database of peptidic foldamers. PMID:31686102
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data. PMID:31614716
DeepScreening: a deep learning-based screening web server for accelerating drug discovery. PMID:31608949
Deciphering the Pharmacological Mechanisms of the Huayu-Qiangshen-Tongbi Formula Through Integrating Network Pharmacology and In Vitro Pharmacological Investigation. PMID:31607918
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features. PMID:31605112
Design and Selection of Novel C1s Inhibitors by In Silico and In Vitro Approaches. PMID:31600984
Cell fishing: A similarity based approach and machine learning strategy for multiple cell lines-compound sensitivity prediction. PMID:31589649
STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products. PMID:31589422
Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. PMID:31576621
BAX, BAK, and BOK: A Coming of Age for the BCL-2 Family Effector Proteins. PMID:31570337
The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu5 receptor case study. PMID:31542869
The Universal 3D QSAR Model for Dopamine D2 Receptor Antagonists. PMID:31540025
Inverse pharmacology: Approaches and tools for introducing druggability into engineered proteins. PMID:31494210
Substance-Based Bibliometrics: Identifying Research Gaps by Counting and Analyzing Substances. PMID:31459314
Data Mining Approach for Extraction of Useful Information About Biologically Active Compounds from Publications. PMID:31453694
Examination of molecular space and feasible structures of bioactive components of humic substances by FTICR MS data mining in ChEMBL database. PMID:31427609
CDEK: Clinical Drug Experience Knowledgebase. PMID:31411687
Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods. PMID:31404334
Novel natural and synthetic inhibitors of solute carriers SGLT1 and SGLT2. PMID:31384471
Artificial Intelligence for Drug Toxicity and Safety. PMID:31383376
Finding Constellations in Chemical Space Through Core Analysis. PMID:31380353
Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1. PMID:31362390
A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria. PMID:31360332
Optimization of Molecules via Deep Reinforcement Learning. PMID:31341196
Targeting HIV/HCV Coinfection Using a Machine Learning-Based Multiple Quantitative Structure-Activity Relationships (Multiple QSAR) Method. PMID:31336592
Insights into Computational Drug Repurposing for Neurodegenerative Disease. PMID:31326236
Chemi-Net: A Molecular Graph Convolutional Network for Accurate Drug Property Prediction. PMID:31295892
Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data. PMID:31292807
Use of big data in drug development for precision medicine: an update. PMID:31286058
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
Exploring the dark genome: implications for precision medicine. PMID:31270560
Influence of the Structural Accuracy of Homology Models on Their Applicability to Docking-Based Virtual Screening: The β2 Adrenergic Receptor as a Case Study. PMID:31257873
A genetics-led approach defines the drug target landscape of 30 immune-related traits. PMID:31253980
MolMeDB: Molecules on Membranes Database. PMID:31250015
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. PMID:31235822
The human endogenous metabolome as a pharmacology baseline for drug discovery. PMID:31226432
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
Validation strategies for target prediction methods. PMID:31220208
Rational design of novel sirtuin 1 activators via structure-activity insights from application of QSAR modeling. PMID:31217784
Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs. PMID:31214240
Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search. PMID:31207991
Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. PMID:31201557
A Systems Pharmacology Approach Uncovers Wogonoside as an Angiogenesis Inhibitor of Triple-Negative Breast Cancer by Targeting Hedgehog Signaling. PMID:31178408
ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK). PMID:31165338
Leveraging heterogeneous data from GHS toxicity annotations, molecular and protein target descriptors and Tox21 assay readouts to predict and rationalise acute toxicity. PMID:31152262
Interlaboratory Variability in Human Hepatocyte Intrinsic Clearance Values and Trends with Physicochemical Properties. PMID:31152241
An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor. PMID:31127405
Auto-Generated Physiological Chain Data for an Ontological Framework for Pharmacology and Mechanism of Action to Determine Suspected Drugs in Cases of Dysuria. PMID:31119651
Informatics and Computational Methods in Natural Product Drug Discovery: A Review and Perspectives. PMID:31114606
Investigating function roles of hypothetical proteins encoded by the Mycobacterium tuberculosis H37Rv genome. PMID:31113361
Drug combination sensitivity scoring facilitates the discovery of synergistic and efficacious drug combinations in cancer. PMID:31107860
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. PMID:31106366
Targeting protein methylation: from chemical tools to precision medicines. PMID:31104094
Tissue-specific genes as an underutilized resource in drug discovery. PMID:31076736
Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases. PMID:31072165
AlloDriver: a method for the identification and analysis of cancer driver targets. PMID:31069394
DrugComb: an integrative cancer drug combination data portal. PMID:31066443
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. PMID:31054028
Analysis and Comparison of Vector Space and Metric Space Representations in QSAR Modeling. PMID:31052325
Diverse Isoquinoline Scaffolds by Ugi/Pomeranz-Fritsch and Ugi/Schlittler-Müller Reactions. PMID:31033297
Extended Multitarget Pharmacology of Anticancer Drugs. PMID:31025863
Genome-wide association study of medication-use and associated disease in the UK Biobank. PMID:31015401
Prediction of Orthosteric and Allosteric Regulations on Cannabinoid Receptors Using Supervised Machine Learning Classifiers. PMID:31013097
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures. PMID:30989574
The EMBL-EBI search and sequence analysis tools APIs in 2019. PMID:30976793
Applications of machine learning in drug discovery and development. PMID:30976107
Assessing the Structural and Pharmacological Similarity of Newly Identified Drugs of Abuse to Controlled Substances Using Public Health Assessment via Structural Evaluation. PMID:30957872
Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. PMID:30956147
Systematic computational identification of promiscuity cliff pathways formed by inhibitors of the human kinome. PMID:30915709
The Light and Dark Sides of Virtual Screening: What Is There to Know? PMID:30893780
Neonicotinoid insecticide design: molecular docking, multiple chemometric approaches, and toxicity relationship with Cowpea aphids. PMID:30877540
Revisiting Histone Deacetylases in Human Tumorigenesis: The Paradigm of Urothelial Bladder Cancer. PMID:30875794
The antimalarial screening landscape-looking beyond the asexual blood stage. PMID:30875617
GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. PMID:30864352
High-throughput screening and Bayesian machine learning for copper-dependent inhibitors of Staphylococcus aureus. PMID:30839007
Free Accessible Databases as a Source of Information about Food Components and Other Compounds with Anticancer Activity⁻Brief Review. PMID:30813234
Ligand biological activity predicted by cleaning positive and negative chemical correlations. PMID:30808733
ADMET-score - a comprehensive scoring function for evaluation of chemical drug-likeness. PMID:30774861
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. PMID:30767155
Ultra-large library docking for discovering new chemotypes. PMID:30728502
The Distribution of Standard Deviations Applied to High Throughput Screening. PMID:30718587
Assessing the public landscape of clinical-stage pharmaceuticals through freely available online databases. PMID:30690196
Reducing Limitation in Probe Design: The Development of a Diazirine-Compatible Suzuki-Miyaura Cross Coupling Reaction. PMID:30655947
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. PMID:30631996
Anti-flavi: A Web Platform to Predict Inhibitors of Flaviviruses Using QSAR and Peptidomimetic Approaches. PMID:30619195
A Computer-Driven Approach to Discover Natural Product Leads for Methicillin-Resistant Staphylococcus aureus Infection Therapy. PMID:30597893
Identifying Potential Ageing-Modulating Drugs In Silico. PMID:30581056
Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin. PMID:30567342
A probabilistic molecular fingerprint for big data settings. PMID:30564943
MER: a shell script and annotation server for minimal named entity recognition and linking. PMID:30519990
Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium. PMID:30482220
Implicit-descriptor ligand-based virtual screening by means of collaborative filtering. PMID:30467684
Open Targets Platform: new developments and updates two years on. PMID:30462303
Predicting Off-Target Binding Profiles With Confidence Using Conformal Prediction. PMID:30459617
Dual Inhibitors of PARPs and ROCKs. PMID:30411017
A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PMID:30408032
Polypharmacology or Promiscuity? Structural Interactions of Resveratrol With Its Bandwagon of Targets. PMID:30405416
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
Comparative genomics of the major parasitic worms. PMID:30397333
Improving Chemical Autoencoder Latent Space and Molecular De Novo Generation Diversity with Heteroencoders. PMID:30380783
DrugCentral 2018: an update. PMID:30371892
PubChem 2019 update: improved access to chemical data. PMID:30371825
Triazolo[4,5-d]pyrimidines as Validated General Control Nonderepressible 2 (GCN2) Protein Kinase Inhibitors Reduce Growth of Leukemia Cells. PMID:30364637
Comparison of Quantitative and Qualitative (Q)SAR Models Created for the Prediction of Ki and IC50 Values of Antitarget Inhibitors. PMID:30364128
Quantitative and systems pharmacology 4. Network-based analysis of drug pleiotropy on coronary artery disease. PMID:30359818
CMAUP: a database of collective molecular activities of useful plants. PMID:30357356
Network-Based Methods for Prediction of Drug-Target Interactions. PMID:30356768
A large-scale dataset of in vivo pharmacology assay results. PMID:30351302
Enhancing Molecular Promiscuity Evaluation Through Assay Profiles. PMID:30338400
Editorial: Drug Repositioning: Current Advances and Future Perspectives. PMID:30294274
Foundations of data-driven medicinal chemistry. PMID:30271612
Target-based drug discovery through inversion of quantitative structure-drug-property relationships and molecular simulation: CA IX-sulphonamide complexes. PMID:30220229
Novel applications of Machine Learning in cheminformatics. PMID:30191348
Homology Modeling Informs Ligand Discovery for the Glutamine Transporter ASCT2. PMID:30137742
Probing the chemical-biological relationship space with the Drug Target Explorer. PMID:30128806
Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors. PMID:30120601
Approaches to target tractability assessment - a practical perspective. PMID:30108951
Computational resources associating diseases with genotypes, phenotypes and exposures. PMID:30102366
Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY. PMID:30087946
SynPharm: A Guide to PHARMACOLOGY Database Tool for Designing Drug Control into Engineered Proteins. PMID:30087931
Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. PMID:30066085
In Silico HCT116 Human Colon Cancer Cell-Based Models En Route to the Discovery of Lead-Like Anticancer Drugs. PMID:30018273
Computational Methodologies in the Exploration of Marine Natural Product Leads. PMID:30011882
A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer's Disease. PMID:29997503
QEX: target-specific druglikeness filter enhances ligand-based virtual screening. PMID:29971617
ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures. PMID:29968796
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. PMID:29943074
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds. PMID:29868550
The Cellosaurus, a Cell-Line Knowledge Resource. PMID:29805321
Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. PMID:29799486
Discovery of Natural Products as Novel and Potent FXR Antagonists by Virtual Screening. PMID:29761098
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. PMID:29757429
Systematic search for benzimidazole compounds and derivatives with antileishmanial effects. PMID:29748853
An Integrated Study on the Antitumor Effect and Mechanism of Triphala Against Gynecological Cancers Based on Network Pharmacological Prediction and In Vitro Experimental Validation. PMID:29742928
A confidence predictor for logD using conformal regression and a support-vector machine. PMID:29616425
Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs. PMID:29541361
In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts. PMID:29515993
Unexplored therapeutic opportunities in the human genome. PMID:29472638
CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds. PMID:29370280
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions. PMID:29276046
Enhancing the Promise of Drug Repositioning through Genetics. PMID:29270124
Objective, Quantitative, Data-Driven Assessment of Chemical Probes. PMID:29249694
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. PMID:29220433
The anthelmintic praziquantel is a human serotoninergic G-protein-coupled receptor ligand. PMID:29208933
Chemoinformatics: a perspective from an academic setting in Latin America. PMID:29204824
Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions. PMID:29186902
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. PMID:29140520
NPASS: natural product activity and species source database for natural product research, discovery and tool development. PMID:29106619
Structure-Based Design and Discovery of New M2 Receptor Agonists. PMID:29094937
Overcoming Obstacles to Drug Repositioning in Japan. PMID:29075191
Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach. PMID:29018348
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization. PMID:28978313
Novel FXa Inhibitor Identification through Integration of Ligand- and Structure-Based Approaches. PMID:28937618
Novel scaffolds for inhibition of Cruzipain identified from high-throughput screening of anti-kinetoplastid chemical boxes. PMID:28935948
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
Identifying relationships between unrelated pharmaceutical target proteins on the basis of shared active compounds. PMID:28884009
Cheminformatic characterization of natural products from Panama. PMID:28831697
Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus. PMID:28779078
A simple mathematical approach to the analysis of polypharmacology and polyspecificity data. PMID:28690829
Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited. PMID:28670471
Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery. PMID:28602100
On the Integration of In Silico Drug Design Methods for Drug Repurposing. PMID:28588497
PPIMpred: a web server for high-throughput screening of small molecules targeting protein-protein interaction. PMID:28484602
The EBI search engine: EBI search as a service-making biological data accessible for all. PMID:28472374
Synthesis, pharmacological evaluation and molecular docking of pyranopyrazole-linked 1,4-dihydropyridines as potent positive inotropes. PMID:28444482
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Virtual screening applications in short-chain dehydrogenase/reductase research. PMID:28286207
The ChEMBL bioactivity database: an update PubMed citations: 489.

489 articles citing: The ChEMBL bioactivity database: an update

DRDB: A Machine Learning Platform to Predict Chemical-Protein Interactions towards Diabetic Retinopathy. PMID:35910835
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Multi-Targeting Approach in Glioblastoma Using Computer-Assisted Drug Discovery Tools to Overcome the Blood-Brain Barrier and Target EGFR/PI3Kp110β Signaling. PMID:35884571
Design and evaluation of pyrimidine derivatives as potent inhibitors of ABCG2, a breast cancer resistance protein. PMID:35875174
Integrated Drug Mining Reveals Actionable Strategies Inhibiting Plexiform Neurofibromas. PMID:35741605
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform. PMID:35710324
Discovery of a High Affinity Adenosine A1/A3 Receptor Antagonist with a Novel 7-Amino-pyrazolo[3,4-d]pyridazine Scaffold. PMID:35707146
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study. PMID:35692045
Molecular Similarity Perception Based on Machine-Learning Models. PMID:35682792
Machine Learning and Its Applications for Protozoal Pathogens and Protozoal Infectious Diseases. PMID:35573796
In Silico Screening of Natural Compounds for Candidates 5HT6 Receptor Antagonists against Alzheimer's Disease. PMID:35565976
The effect of the intramolecular C-H⋯O interactions on the conformational preferences of bis-arylsulfones - 5-HT6 receptor antagonists and beyond. PMID:35541096
Discovery of Cobimetinib as a novel A-FABP inhibitor using machine learning and molecular docking-based virtual screening. PMID:35520131
ExPheWas: a platform for cis-Mendelian randomization and gene-based association scans. PMID:35474380
Differentiating Inhibitors of Closely Related Protein Kinases with Single- or Multi-Target Activity via Explainable Machine Learning and Feature Analysis. PMID:35454147
Introducing a Chemically Intuitive Core-Substituent Fingerprint Designed to Explore Structural Requirements for Effective Similarity Searching and Machine Learning. PMID:35408730
Explaining and avoiding failure modes in goal-directed generation of small molecules. PMID:35365218
Evaluation of Blood-Brain-Barrier Permeability, Neurotoxicity, and Potential Cognitive Impairment by Pseudomonas aeruginosa's Virulence Factor Pyocyanin. PMID:35340215
Prediction of the Neurotoxic Potential of Chemicals Based on Modelling of Molecular Initiating Events Upstream of the Adverse Outcome Pathways of (Developmental) Neurotoxicity. PMID:35328472
Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. PMID:35323700
Candidate Therapeutics by Screening for Multitargeting Ligands: Combining the CB2 Receptor With CB1, PPARγ and 5-HT4 Receptors. PMID:35295337
The Pandemic Response Box─Accelerating Drug Discovery Efforts after Disease Outbreaks. PMID:35286809
On the Value of Using 3D Shape and Electrostatic Similarities in Deep Generative Methods. PMID:35271260
The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization. PMID:35193494
The Pseudo-Natural Product Rhonin Targets RHOGDI. PMID:35170181
Approach for the Design of Covalent Protein Kinase Inhibitors via Focused Deep Generative Modeling. PMID:35056884
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer. PMID:35035776
Mining Clinical Data for Novel Posttraumatic Stress Disorder Medications. PMID:34952698
Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. PMID:34946572
pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. PMID:34901870
CRNNTL: Convolutional Recurrent Neural Network and Transfer Learning for QSAR Modeling in Organic Drug and Material Discovery. PMID:34885843
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Prediction of Anti-Glioblastoma Drug-Decorated Nanoparticle Delivery Systems Using Molecular Descriptors and Machine Learning. PMID:34768951
Artificial Intelligence and Quantum Computing as the Next Pharma Disruptors. PMID:34731476
Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs. PMID:34721010
SARS-CoV-2-host proteome interactions for antiviral drug discovery. PMID:34709727
Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. PMID:34705221
Individual and collective human intelligence in drug design: evaluating the search strategy. PMID:34635158
Representation of molecules for drug response prediction. PMID:34571534
Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery. PMID:34554348
Coumarins as Tool Compounds to Aid the Discovery of Selective Function Modulators of Steroid Hormone Binding Proteins. PMID:34500576
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
De novo molecular drug design benchmarking. PMID:34458735
Pharmacophore-Based Virtual Screening, Quantum Mechanics Calculations, and Molecular Dynamics Simulation Approaches Identified Potential Natural Antiviral Drug Candidates against MERS-CoV S1-NTD. PMID:34443556
Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty. PMID:34412708
Prediction of Molecular Properties Using Molecular Topographic Map. PMID:34361624
Facing small and biased data dilemma in drug discovery with enhanced federated learning approaches. PMID:34319533
Beam Search for Automated Design and Scoring of Novel ROR Ligands with Machine Intelligence*. PMID:34165856
Neural network activation similarity: a new measure to assist decision making in chemical toxicology. PMID:34123016
Molecular mechanisms of metabotropic GABAB receptor function. PMID:34049877
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Small-Molecule Inhibitors of the RNA M6A Demethylases FTO Potently Support the Survival of Dopamine Neurons. PMID:33926120
A computational method for drug sensitivity prediction of cancer cell lines based on various molecular information. PMID:33914775
Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection. PMID:33892799
Prediction of Anti-COVID 19 Therapeutic Power of Medicinal Moroccan Plants Using Molecular Docking. PMID:33888980
Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors. PMID:33856768
Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. PMID:33856591
PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning. PMID:33851095
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
QSAR-Based Virtual Screening of Natural Products Database for Identification of Potent Antimalarial Hits. PMID:33808643
Nα-1, 3-Benzenedicarbonyl-Bis-(Amino Acid) and Dipeptide Candidates: Synthesis, Cytotoxic, Antimicrobial and Molecular Docking Investigation. PMID:33790542
Natural product fragment combination to performance-diverse pseudo-natural products. PMID:33767198
Physicochemical Profiling and Comparison of Research Antiplasmodials and Advanced Stage Antimalarials with Oral Drugs. PMID:33718733
Adapting the DeepSARM approach for dual-target ligand design. PMID:33712972
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. PMID:33709119
Expanding the drug discovery space with predicted metabolite-target interactions. PMID:33674782
Fast Identification of Adverse Drug Reactions (ADRs) of Digestive and Nervous Systems of Organic Drugs by In Silico Models. PMID:33578679
A Multi-Objective Approach for Drug Repurposing in Preeclampsia. PMID:33546161
Generating Property-Matched Decoy Molecules Using Deep Learning. PMID:33532838
Anti-proliferative and apoptotic effects of hull-less pumpkin extract on human papillary thyroid carcinoma cell line. PMID:33504684
Property-Unmatched Decoys in Docking Benchmarks. PMID:33494610
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. PMID:33431038
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. PMID:33431036
Quantitative prediction of selectivity between the A1 and A2A adenosine receptors. PMID:33431012
SmartGraph: a network pharmacology investigation platform. PMID:33430980
Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies. PMID:33430967
Design and Application in Delivery System of Intranasal Antidepressants. PMID:33409272
A unique ligand-steered strategy for CC chemokine receptor 2 homology modeling to facilitate structure-based virtual screening. PMID:33386704
OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. PMID:33361798
Design and Synthesis of DDR1 Inhibitors with a Desired Pharmacophore Using Deep Generative Models. PMID:33289306
Systematic Assessment of Fragment Identification for Multitarget Drug Design. PMID:33283450
Virtual screening and drug repurposing experiments to identify potential novel selective MAO-B inhibitors for Parkinson's disease treatment. PMID:33237524
Identification and Validation of Carbonic Anhydrase II as the First Target of the Anti-Inflammatory Drug Actarit. PMID:33227945
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
A network pharmacology-based approach to explore potential targets of Caesalpinia pulcherima: an updated prototype in drug discovery. PMID:33057155
Enhancing scientific discoveries in molecular biology with deep generative models. PMID:32975352
Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. PMID:32931270
Prediction of an MMP-1 inhibitor activity cliff using the SAR matrix approach and its experimental validation. PMID:32895466
Mining Public Domain Data to Develop Selective DYRK1A Inhibitors. PMID:32832032
Chemoinformatic studies on some inhibitors of dopamine transporter and the receptor targeting schizophrenia for developing novel antipsychotic agents. PMID:32760824
Prediction of Antimalarial Drug-Decorated Nanoparticle Delivery Systems with Random Forest Models. PMID:32751710
HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. PMID:32746900
Cheminformatics in Natural Product-based Drug Discovery. PMID:32725781
A Pilot Study of Multi-Input Recurrent Neural Networks for Drug-Kinase Binding Prediction. PMID:32722290
Drug-target interactions prediction using marginalized denoising model on heterogeneous networks. PMID:32703151
Pruned Machine Learning Models to Predict Aqueous Solubility. PMID:32685821
A simple open source bioinformatic methodology for initial exploration of GPCR ligands' agonistic/antagonistic properties. PMID:32662237
Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition. PMID:32645448
Computer-Aided Fragment Growing Strategies to Design Dual Inhibitors of Soluble Epoxide Hydrolase and LTA4 Hydrolase. PMID:32551007
De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PMID:32453724
Structure-Based Virtual Screening: From Classical to Artificial Intelligence. PMID:32411671
Virtual Screening and the In Vitro Assessment of the Antileishmanial Activity of Lignans. PMID:32408657
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. PMID:32343143
Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells. PMID:32325755
Accelerated Discovery of Novel Ponatinib Analogs with Improved Properties for the Treatment of Parkinson's Disease. PMID:32292555
Cheminformatics Analysis and Modeling with MacrolactoneDB. PMID:32286395
From SAR Diagnostics to Compound Design: Development Chronology of the Compound Optimization Monitor (COMO) Method. PMID:32282989
The SAR Matrix Method and an Artificially Intelligent Variant for the Identification and Structural Organization of Analog Series, SAR Analysis, and Compound Design. PMID:32271994
Machine Learning Uncovers Food- and Excipient-Drug Interactions. PMID:32187543
Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity. PMID:32168319
A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands. PMID:32112287
Phenotyping Reveals Targets of a Pseudo-Natural-Product Autophagy Inhibitor. PMID:32108411
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. PMID:32040955
DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. PMID:32035227
Cinnamic Derivatives as Antitubercular Agents: Characterization by Quantitative Structure-Activity Relationship Studies. PMID:31973244
Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction. PMID:31960253
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. PMID:31950972
A prospective compound screening contest identified broader inhibitors for Sirtuin 1. PMID:31863054
A platform for target prediction of phenotypic screening hit molecules. PMID:31836397
Deep learning of pharmacogenomics resources: moving towards precision oncology. PMID:31813953
Elucidating the active δ-opioid receptor crystal structure with peptide and small-molecule agonists. PMID:31807708
Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer. PMID:31752564
Structural insights into melatonin receptors. PMID:31693784
Synthetic Activators of Cell Migration Designed by Constructive Machine Learning. PMID:31660283
A Network Pharmacology Study of the Multi-Targeting Profile of an Antiarrhythmic Chinese Medicine Xin Su Ning. PMID:31607935
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. PMID:31598897
Large-Scale Comparison of Alternative Similarity Search Strategies with Varying Chemical Information Contents. PMID:31552377
Benchmarking network propagation methods for disease gene identification. PMID:31479437
Synthesis of Indomorphan Pseudo-Natural Product Inhibitors of Glucose Transporters GLUT-1 and -3. PMID:31469221
An Insight Into the Molecular Mechanism of Berberine Towards Multiple Cancer Types Through Systems Pharmacology. PMID:31447670
Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships. PMID:31435894
Reliable Target Prediction of Bioactive Molecules Based on Chemical Similarity Without Employing Statistical Methods. PMID:31404334
Binding site characterization - similarity, promiscuity, and druggability. PMID:31391887
Acetaminophen Overdose as a Potential Risk Factor for Parkinson's Disease. PMID:31305025
Ligand-guided homology modeling drives identification of novel histamine H3 receptor ligands. PMID:31237914
Identification of small molecule enzyme inhibitors as broad-spectrum anthelmintics. PMID:31235822
Accelerating Drug Discovery by Early Protein Drug Target Prediction Based on a Multi-Fingerprint Similarity Search. PMID:31207991
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences. PMID:31199797
A Structure-Based Drug Discovery Paradigm. PMID:31174387
Machine Learning for Molecular Modelling in Drug Design. PMID:31167503
Mapping the Azolog Space Enables the Optical Control of New Biological Targets. PMID:31041380
Navigating in vitro bioactivity data by investigating available resources using model compounds. PMID:31036807
Extended Multitarget Pharmacology of Anticancer Drugs. PMID:31025863
Structural basis of ligand recognition at the human MT1 melatonin receptor. PMID:31019306
XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. PMID:31019305
Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science. PMID:30976382
Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. PMID:30956147
Idea2Data: Toward a New Paradigm for Drug Discovery. PMID:30891127
Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations. PMID:30842833
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation. PMID:30840169
Drug-Membrane Permeability across Chemical Space. PMID:30834317
Drug repurposing for antimicrobial discovery. PMID:30833727
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Antibacterial activity of synthetic 1,3-bis(aryloxy)propan-2-amines against Gram-positive bacteria. PMID:30773849
Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling. PMID:30767155
Enhanced taxonomy annotation of antiviral activity data from ChEMBL. PMID:30753475
Predicting clinically promising therapeutic hypotheses using tensor factorization. PMID:30736745
Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research. PMID:30727895
Discovering highly selective and diverse PPAR-delta agonists by ligand based machine learning and structural modeling. PMID:30705343
Automatic identification of relevant chemical compounds from patents. PMID:30698776
NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules. PMID:30682850
Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space. PMID:30648156
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. PMID:30631996
Discovery of Novel Molecular Frameworks of Farnesoid X Receptor Modulators by Ensemble Machine Learning. PMID:30622878
Use of a Bioinformatics-Based Toxicity Scoring System to Assess Serotonin Burden and Predict Population-Level Adverse Drug Events from Concomitant Serotonergic Drug Therapy. PMID:30620414
FABP4 inhibitors 3D-QSAR model and isosteric replacement of BMS309403 datasets. PMID:30619925
The integration of pharmacophore-based 3D QSAR modeling and virtual screening in safety profiling: A case study to identify antagonistic activities against adenosine receptor, A2A, using 1,897 known drugs. PMID:30605479
Screening the Pathogen Box for Identification of New Chemical Agents with Anti-Fasciola hepatica Activity. PMID:30602522
Epigenome-wide meta-analysis of DNA methylation and childhood asthma. PMID:30579849
Search for a 5-CT alternative. In vitro and in vivo evaluation of novel pharmacological tools: 3-(1-alkyl-1H-imidazol-5-yl)-1H-indole-5-carboxamides, low-basicity 5-HT7 receptor agonists. PMID:30568756
Computational Assessment of Chemical Saturation of Analogue Series under Varying Conditions. PMID:30556013
PDX Finder: A portal for patient-derived tumor xenograft model discovery. PMID:30535239
High-throughput screening for selective appetite modulators: A multibehavioral and translational drug discovery strategy. PMID:30402545
ChEMBL: towards direct deposition of bioassay data. PMID:30398643
Integrative Data Mining, Scaffold Analysis, and Sequential Binary Classification Models for Exploring Ligand Profiles of Hepatic Organic Anion Transporting Polypeptides. PMID:30372058
A large-scale dataset of in vivo pharmacology assay results. PMID:30351302
Strategies to Obtain Encapsulation and Controlled Release of Pentamidine in Mesoporous Silica Nanoparticles. PMID:30347763
Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents. PMID:30346968
Rationalizing Secondary Pharmacology Screening Using Human Genetic and Pharmacological Evidence. PMID:30346593
The Pioglitazone Trek via Human PPAR Gamma: From Discovery to a Medicine at the FDA and Beyond. PMID:30337873
Experimentally Validated Pharmacoinformatics Approach to Predict hERG Inhibition Potential of New Chemical Entities. PMID:30333745
Kororamides, Convolutamines, and Indole Derivatives as Possible Tau and Dual-Specificity Kinase Inhibitors for Alzheimer's Disease: A Computational Study. PMID:30332805
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. PMID:30321373
Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. PMID:30319692
Deep learning and virtual drug screening. PMID:30288997
Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation. PMID:30202014
Discovery of High-Affinity Cannabinoid Receptors Ligands through a 3D-QSAR Ushered by Scaffold-Hopping Analysis. PMID:30200181
Five Years of the KNIME Vernalis Cheminformatics Community Contribution. PMID:30182834
Large-scale comparison of machine learning methods for drug target prediction on ChEMBL. PMID:30155234
Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors. PMID:30155037
Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design. PMID:30151082
Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. PMID:30123424
In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1). PMID:30109440
Oral drug suitability parameters. PMID:30108936
3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. PMID:30108817
Designing safer oral drugs. PMID:30108773
The Recognition of Unrelated Ligands by Identical Proteins. PMID:30095890
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. PMID:30094533
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. PMID:30084866
PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. PMID:30053271
Deep reinforcement learning for de novo drug design. PMID:30050984
Novel pharmacological maps of protein lysine methyltransferases: key for target deorphanization. PMID:30032331
Prediction of Compound Profiling Matrices Using Machine Learning. PMID:30023899
Extracting Compound Profiling Matrices from Screening Data. PMID:30023898
Novel Adamantanyl-Based Thiadiazolyl Pyrazoles Targeting EGFR in Triple-Negative Breast Cancer. PMID:30023509
In Silico Workflow for the Discovery of Natural Products Activating the G Protein-Coupled Bile Acid Receptor 1. PMID:30013964
Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. PMID:30013184
Thiodipeptides targeting the intestinal oligopeptide transporter as a general approach to improving oral drug delivery. PMID:30006163
ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy. PMID:29993812
Conformational ensemble comparison for small molecules in drug discovery. PMID:29987709
Implications of Off-Target Serotoninergic Drug Activity: An Analysis of Serotonin Syndrome Reports Using a Systematic Bioinformatics Approach. PMID:29972695
QEX: target-specific druglikeness filter enhances ligand-based virtual screening. PMID:29971617
Gene expression-based drug repurposing to target aging. PMID:29959820
Systems-Based Interactome Analysis for Hematopoiesis Effect of Angelicae sinensis Radix: Regulated Network of Cell Proliferation towards Hemopoiesis. PMID:29943236
Systematic Mendelian randomization framework elucidates hundreds of CpG sites which may mediate the influence of genetic variants on disease. PMID:29893838
Exploring Landscape of Drug-Target-Pathway-Side Effect Associations. PMID:29888057
GNOMICS: A one-stop shop for biomedical and genomic data. PMID:29888054
Machine Learning-based Virtual Screening and Its Applications to Alzheimer's Drug Discovery: A Review. PMID:29879881
Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells. PMID:29867139
Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery. PMID:29799486
Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease. PMID:29792714
Effect of missing data on multitask prediction methods. PMID:29789977
Substructural Connectivity Fingerprint and Extreme Entropy Machines-A New Method of Compound Representation and Analysis. PMID:29789513
How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors. PMID:29755970
Systematic search for benzimidazole compounds and derivatives with antileishmanial effects. PMID:29748853
Fingerprint-Based Machine Learning Approach to Identify Potent and Selective 5-HT2BR Ligands. PMID:29748476
The Mu.Ta.Lig. Chemotheca: A Community-Populated Molecular Database for Multi-Target Ligands Identification and Compound-Repurposing. PMID:29725591
ProTox-II: a webserver for the prediction of toxicity of chemicals. PMID:29718510
Maximal Unbiased Benchmarking Data Sets for Human Chemokine Receptors and Comparative Analysis. PMID:29698608
Community-driven roadmap for integrated disease maps. PMID:29688273
Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. PMID:29672063
Data Mining and Computational Modeling of High-Throughput Screening Datasets. PMID:29671272
PKIDB: A Curated, Annotated and Updated Database of Protein Kinase Inhibitors in Clinical Trials. PMID:29662024
Drug Repositioning in Glioblastoma: A Pathway Perspective. PMID:29615902
In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum. PMID:29584709
HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors. PMID:29524011
Analysis of a gene panel for targeted sequencing of colorectal cancer samples. PMID:29507673
Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PMID:29444113
Decoys Selection in Benchmarking Datasets: Overview and Perspectives. PMID:29416509
5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology. PMID:29398112
Classifiers and their Metrics Quantified. PMID:29360259
An automated framework for QSAR model building. PMID:29340790
3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. PMID:29337438
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. PMID:29335872
Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain. PMID:29321504
De Novo Design of Bioactive Small Molecules by Artificial Intelligence. PMID:29319225
G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs? PMID:29298813
Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server. PMID:29297315
Congestion game scheduling for virtual drug screening optimization. PMID:29264790
vNN Web Server for ADMET Predictions. PMID:29255418
NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy. PMID:29220436
An unexpected switch in peptide binding mode: from simulation to substrate specificity. PMID:29210603
Target and Tissue Selectivity Prediction by Integrated Mechanistic Pharmacokinetic-Target Binding and Quantitative Structure Activity Modeling. PMID:29204742
Predicted Biological Activity of Purchasable Chemical Space. PMID:29193970
The target landscape of clinical kinase drugs. PMID:29191878
Computer-Aided Drug Design Applied to Marine Drug Discovery: Meridianins as Alzheimer's Disease Therapeutic Agents. PMID:29186912
The CompTox Chemistry Dashboard: a community data resource for environmental chemistry. PMID:29185060
Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91. PMID:29157600
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. PMID:29156001
GPCRdb in 2018: adding GPCR structure models and ligands. PMID:29155946
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. PMID:29149325
ECOdrug: a database connecting drugs and conservation of their targets across species. PMID:29140522
SuperDRUG2: a one stop resource for approved/marketed drugs. PMID:29140469
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. PMID:29126160
Are there physicochemical differences between allosteric and competitive ligands? PMID:29125840
Quantitative and Systems Pharmacology 3. Network-Based Identification of New Targets for Natural Products Enables Potential Uses in Aging-Associated Disorders. PMID:29093681
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. PMID:29086168
Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses. PMID:29086108
Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data. PMID:29086090
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. PMID:29086040
The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production. PMID:29062930
Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and DrugMatrix datasets. PMID:29062063
D4 dopamine receptor high-resolution structures enable the discovery of selective agonists. PMID:29051383
Report and Application of a Tool Compound Data Set. PMID:29035535
Evidence-Based Precision Oncology with the Cancer Targetome. PMID:28964549
Orthologue chemical space and its influence on target prediction. PMID:28961699
Quantitative and Systems Pharmacology. 1. In Silico Prediction of Drug-Target Interactions of Natural Products Enables New Targeted Cancer Therapy. PMID:28956927
Human hepatic gene expression signature of non-alcoholic fatty liver disease progression, a meta-analysis. PMID:28955037
An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. PMID:28931921
The role of polycarbonate monomer bisphenol-A in insulin resistance. PMID:28929027
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns. PMID:28900272
Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity. PMID:28894419
Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2. PMID:28889350
Forbidden Coherence Transfer of 19F Nuclei to Quantitatively Measure the Dynamics of a CF₃-Containing Ligand in Receptor-Bound States. PMID:28880244
Structural and Functional View of Polypharmacology. PMID:28860623
In silico prediction of novel therapeutic targets using gene-disease association data. PMID:28851378
Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. PMID:28834292
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors. PMID:28787438
The Microphysiology Systems Database for Analyzing and Modeling Compound Interactions with Human and Animal Organ Models. PMID:28781990
A Simple Representation of Three-Dimensional Molecular Structure. PMID:28731335
Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations. PMID:28730498
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Exploring anti-malarial potential of FDA approved drugs: an in silico approach. PMID:28720135
Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach. PMID:28690380
DeCAF-Discrimination, Comparison, Alignment Tool for 2D PHarmacophores. PMID:28684712
Classification and analysis of a large collection of in vivo bioassay descriptions. PMID:28678787
Predicting the Reliability of Drug-target Interaction Predictions with Maximum Coverage of Target Space. PMID:28630414
Systematic Data Mining Reveals Synergistic H3R/MCHR1 Ligands. PMID:28626527
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
Large-Scale Prediction of Drug-Target Interaction: a Data-Centric Review. PMID:28577120
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
An in silico high-throughput screen identifies potential selective inhibitors for the non-receptor tyrosine kinase Pyk2. PMID:28572720
Privileged Structures Revisited. PMID:28558125
Similarity- and Substructure-Based Development of β2-Adrenergic Receptor Ligands Based on Unusual Scaffolds. PMID:28523097
Low-basicity 5-HT7 Receptor Agonists Synthesized Using the van Leusen Multicomponent Protocol. PMID:28473721
A PanorOmic view of personal cancer genomes. PMID:28453651
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. PMID:28431173
Scaffold Diversity of Fungal Metabolites. PMID:28420994
Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. PMID:28397808
Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds. PMID:28376613
Structure-Based Target-Specific Screening Leads to Small-Molecule CaMKII Inhibitors. PMID:28371191
Spresso: an ultrafast compound pre-screening method based on compound decomposition. PMID:28369284
Better living through ontologies at the Immune Epitope Database. PMID:28365732
The druggable genome and support for target identification and validation in drug development. PMID:28356508
PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing. PMID:28346087
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. PMID:28316655
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. PMID:28296354
Systems Pharmacology-Based Discovery of Natural Products for Precision Oncology Through Targeting Cancer Mutated Genes. PMID:28294568
Docking-based virtual screening of Brazilian natural compounds using the OOMT as the pharmacological target database. PMID:28285443
How Open Data Shapes In Silico Transporter Modeling. PMID:28272367
Structure-Promiscuity Relationship Puzzles-Extensively Assayed Analogs with Large Differences in Target Annotations. PMID:28265982
Practical application of the Average Information Content Maximization (AIC-MAX) algorithm: selection of the most important structural features for serotonin receptor ligands. PMID:28185036
An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge. PMID:28158609
Protein Bioinformatics Databases and Resources. PMID:28150231
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. PMID:28125221
Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors. PMID:28108896
Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery. PMID:28063110
KinMap: a web-based tool for interactive navigation through human kinome data. PMID:28056780
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
HEDD: the human epigenetic drug database. PMID:28025347
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. PMID:28025336
VaProS: a database-integration approach for protein/genome information retrieval. PMID:28012137
Computational chemistry at Janssen. PMID:27995515
ReconMap: an interactive visualization of human metabolism. PMID:27993782
Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. PMID:27992882
Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science. PMID:27929431
Identification of critical paralog groups with indispensable roles in the regulation of signaling flow. PMID:27922122
A comprehensive map of molecular drug targets. PMID:27910877
Pharos: Collating protein information to shed light on the druggable genome. PMID:27903890
Open Targets: a platform for therapeutic target identification and validation. PMID:27899665
PubChem BioAssay: 2017 update. PMID:27899599
The ChEMBL database in 2017. PMID:27899562
WormBase ParaSite - a comprehensive resource for helminth genomics. PMID:27899279
From linked open data to molecular interaction: studying selectivity trends for ligands of the human serotonin and dopamine transporter. PMID:27891211
Predicting protein-ligand affinity with a random matrix framework. PMID:27856761
Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery. PMID:27798721
DrugCentral: online drug compendium. PMID:27789690
Compilation and physicochemical classification analysis of a diverse hERG inhibition database. PMID:27783199
Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. PMID:27774140
Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing. PMID:27716836
3D structure prediction of histone acetyltransferase proteins of the MYST family and their interactome in Arabidopsis thaliana. PMID:27709438
Docking-undocking combination applied to the D3R Grand Challenge 2015. PMID:27709317
A machine-learned computational functional genomics-based approach to drug classification. PMID:27695919
A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. PMID:27678076
Identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining. PMID:27653775
Computer-aided drug design at Boehringer Ingelheim. PMID:27650777
StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. PMID:27643925
A COL11A1-correlated pan-cancer gene signature of activated fibroblasts for the prioritization of therapeutic targets. PMID:27609069
The health care and life sciences community profile for dataset descriptions. PMID:27602295
A D3R prospective evaluation of machine learning for protein-ligand scoring. PMID:27592011
HOMCOS: an updated server to search and model complex 3D structures. PMID:27522608
MMpI: A WideRange of Available Compounds of Matrix Metalloproteinase Inhibitors. PMID:27509041
AVCpred: an integrated web server for prediction and design of antiviral compounds. PMID:27490990
Identification of Novel Smoothened Ligands Using Structure-Based Docking. PMID:27490099
Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? PMID:27482722
Getting the most out of PubChem for virtual screening. PMID:27454129
Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. PMID:27439119
Computational predictive models for P-glycoprotein inhibition of in-house chalcone derivatives and drug-bank compounds. PMID:27431577
Virtual Screening of DrugBank Reveals Two Drugs as New BCRP Inhibitors. PMID:27401583
Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review. PMID:27401223
Comparing structural fingerprints using a literature-based similarity benchmark. PMID:27382417
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge. PMID:27306312
Ring system-based chemical graph generation for de novo molecular design. PMID:27299746
Literature information in PubChem: associations between PubChem records and scientific articles. PMID:27293485
Are the physicochemical properties of antibacterial compounds really different from other drugs? PMID:27274770
Counting on natural products for drug design. PMID:27219696
An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations. PMID:27196054
How Reliable Are Ligand-Centric Methods for Target Fishing? PMID:27148522
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. PMID:27141091
systemsDock: a web server for network pharmacology-based prediction and analysis. PMID:27131384
MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs. PMID:27131358
A quantitative threshold for high/low extent of urinary excretion of compounds in humans. PMID:27122230
Development of a web-based tool for automated processing and cataloging of a unique combinatorial drug screen. PMID:27117032
Improving chemical similarity ensemble approach in target prediction. PMID:27110288
USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques. PMID:27106057
Determining the Degree of Promiscuity of Extensively Assayed Compounds. PMID:27082988
In silico methods for drug repurposing and pharmacology. PMID:27080087
Impact of similarity threshold on the topology of molecular similarity networks and clustering outcomes. PMID:27030802
In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PMID:26963248
Endothelin. PMID:26956245
Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PMID:26954019
Combinatorial phenotypic screen uncovers unrecognized family of extended thiourea inhibitors with copper-dependent anti-staphylococcal activity. PMID:26935206
A new approach to chemotherapy: drug-induced differentiation kills African trypanosomes. PMID:26931380
AnalogExplorer2 - Stereochemistry sensitive graphical analysis of large analog series. PMID:26913194
From Drug Screening to Target Deconvolution: a Target-Based Drug Discovery Pipeline Using Leishmania Casein Kinase 1 Isoform 2 To Identify Compounds with Antileishmanial Activity. PMID:26902771
Simvastatin Sodium Salt and Fluvastatin Interact with Human Gap Junction Gamma-3 Protein. PMID:26863535
Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. PMID:26855674
Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. PMID:26841718
Self Organizing Map-Based Classification of Cathepsin k and S Inhibitors with Different Selectivity Profiles Using Different Structural Molecular Fingerprints: Design and Application for Discovery of Novel Hits. PMID:26840291
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. PMID:26829384
A multiple kernel learning algorithm for drug-target interaction prediction. PMID:26801218
Average Information Content Maximization--A New Approach for Fingerprint Hybridization and Reduction. PMID:26784447
Plasma urate concentration and risk of coronary heart disease: a Mendelian randomisation analysis. PMID:26781229
Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses. PMID:26750305
Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions. PMID:26726827
Benzobisthiazoles Represent a Novel Scaffold for Kinase Inhibitors of CLK Family Members. PMID:26701387
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Predictive Modeling of Drug Treatment in the Area of Personalized Medicine. PMID:26692759
Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PMID:26642067
High-quality and universal empirical atomic charges for chemoinformatics applications. PMID:26633997
Repositioning of Thiourea-Containing Drugs as Tyrosinase Inhibitors. PMID:26633377
CancerResource--updated database of cancer-relevant proteins, mutations and interacting drugs. PMID:26590406
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. PMID:26590256
SureChEMBL: a large-scale, chemically annotated patent document database. PMID:26582922
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors. PMID:26560977
WITHDRAWN--a resource for withdrawn and discontinued drugs. PMID:26553801
DGIdb 2.0: mining clinically relevant drug-gene interactions. PMID:26531824
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Can Invalid Bioactives Undermine Natural Product-Based Drug Discovery? PMID:26505758
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. PMID:26504143
Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications. PMID:26501781
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. PMID:26481362
ZINC 15--Ligand Discovery for Everyone. PMID:26479676
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. PMID:26476444
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. PMID:26464438
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. PMID:26435758
Predicting Mouse Liver Microsomal Stability with "Pruned" Machine Learning Models and Public Data. PMID:26415647
PubChem Substance and Compound databases. PMID:26400175
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. PMID:26384374
The Mechanism Research of Qishen Yiqi Formula by Module-Network Analysis. PMID:26379745
Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference. PMID:26352211
Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science. PMID:26340620
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design. PMID:26335248
Computational approaches to natural product discovery. PMID:26284671
Minimum Information about a Biosynthetic Gene cluster. PMID:26284661
JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing. PMID:26280450
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. PMID:26206305
Molecular docking and structure-based drug design strategies. PMID:26205061
Activity, assay and target data curation and quality in the ChEMBL database. PMID:26201396
Making Transporter Models for Drug-Drug Interaction Prediction Mobile. PMID:26199424
Reporting biological assay screening results for maximum impact. PMID:26194585
Expanding opportunities for mining bioactive chemistry from patents. PMID:26194581
A large-scale crop protection bioassay data set. PMID:26175909
Discovery of a Novel HDAC2 Inhibitor by a Scaffold-Merging Hybrid Query. PMID:26144283
Antibiotic-modifying activity of riachin, a non-cyanogenic cyanoglycoside extracted from Bauhinia pentandra. PMID:26109849
Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites. PMID:26029108
Quantifying the tendency of therapeutic target proteins to bind promiscuous or selective compounds. PMID:26000736
Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. PMID:25994950
The relationship between target-class and the physicochemical properties of antibacterial drugs. PMID:25975639
ADME SARfari: comparative genomics of drug metabolizing systems. PMID:25964657
Galahad: a web server for drug effect analysis from gene expression. PMID:25940630
ChEMBL web services: streamlining access to drug discovery data and utilities. PMID:25883136
In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv). PMID:25811866
Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation. PMID:25799414
Prediction of drug-ABC-transporter interaction--Recent advances and future challenges. PMID:25769815
Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts. PMID:25760829
Development of data representation standards by the human proteome organization proteomics standards initiative. PMID:25726569
Structural and Activity Profile Relationships Between Drug Scaffolds. PMID:25697829
Developing a molecular roadmap of drug-food interactions. PMID:25668218
Flexibility and small pockets at protein-protein interfaces: New insights into druggability. PMID:25662442
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study. PMID:25652942
Virus-host interactomics: new insights and opportunities for antiviral drug discovery. PMID:25593595
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. PMID:25571995
The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PMID:25522365
Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. PMID:25520777
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. PMID:25414339
The eTOX data-sharing project to advance in silico drug-induced toxicity prediction. PMID:25405742
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. PMID:25404129
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. PMID:25392426
PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains. PMID:25348214
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. PMID:25221628
A document classifier for medicinal chemistry publications trained on the ChEMBL corpus. PMID:25221627
The essential roles of chemistry in high-throughput screening triage. PMID:25163000
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Evolving BioAssay Ontology (BAO): modularization, integration and applications. PMID:25093074
Drug repurposing and human parasitic protozoan diseases. PMID:25057459
In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion. PMID:24976868
Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. PMID:24886433
SwissTargetPrediction: a web server for target prediction of bioactive small molecules. PMID:24792161
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. PMID:24644270
ChEMBL: towards direct deposition of bioassay data PubMed citations: 291.

291 articles citing: ChEMBL: towards direct deposition of bioassay data

Integrating concept of pharmacophore with graph neural networks for chemical property prediction and interpretation. PMID:35927691
Evaluating the efficacy and mechanism of metformin targets on reducing Alzheimer's disease risk in the general population: a Mendelian randomisation study. PMID:35902387
Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors. PMID:35897894
Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders. PMID:35890359
Do AutoML-Based QSAR Models Fulfill OECD Principles for Regulatory Assessment? A 5-HT1A Receptor Case. PMID:35890310
Protein-Ligand Docking in the Machine-Learning Era. PMID:35889440
Structure Prediction, Evaluation, and Validation of GPR18 Lipid Receptor Using Free Programs. PMID:35887268
Graph-based molecular Pareto optimisation. PMID:35872811
Predicting compound-protein interaction using hierarchical graph convolutional networks. PMID:35862351
Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Blood-brain barrier penetration prediction enhanced by uncertainty estimation. PMID:35799215
A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19. PMID:35777222
Identification of Five Hub Genes Based on Single-Cell RNA Sequencing Data and Network Pharmacology in Patients With Acute Myocardial Infarction. PMID:35757636
Toward in Silico Modeling of Dynamic Combinatorial Libraries. PMID:35756377
Systematic indication extension for drugs using patient stratification insights generated by combinatorial analytics. PMID:35755863
Identifying Possible AChE Inhibitors from Drug-like Molecules via Machine Learning and Experimental Studies. PMID:35755364
Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. PMID:35733108
Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. PMID:35725381
Identifying RO9021 as a Potential Inhibitor of PknG from Mycobacterium tuberculosis: Combinative Computational and In Vitro Studies. PMID:35721990
StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit. PMID:35711912
The chemistry of snake venom and its medicinal potential. PMID:35702592
Public Data Set of Protein-Ligand Dissociation Kinetic Constants for Quantitative Structure-Kinetics Relationship Studies. PMID:35694511
KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study. PMID:35692045
QMugs, quantum mechanical properties of drug-like molecules. PMID:35672335
Computational Discovery of Cancer Immunotherapy Targets by Intercellular CRISPR Screens. PMID:35651625
canSAR chemistry registration and standardization pipeline. PMID:35643512
Phenotypic drug discovery: recent successes, lessons learned and new directions. PMID:35637317
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions. PMID:35610036
Machine Learning in Antibacterial Drug Design. PMID:35592425
Predicting target-ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery. PMID:35589824
Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions. PMID:35579568
7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1. PMID:35566242
PLATO: A Predictive Drug Discovery Web Platform for Efficient Target Fishing and Bioactivity Profiling of Small Molecules. PMID:35563636
Hierarchical network analysis of co-occurring bioentities in literature. PMID:35550589
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. PMID:35524571
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. PMID:35524557
SuperPred 3.0: drug classification and target prediction-a machine learning approach. PMID:35524552
Discovery of Cobimetinib as a novel A-FABP inhibitor using machine learning and molecular docking-based virtual screening. PMID:35520131
cheML.io: an online database of ML-generated molecules. PMID:35516285
Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data. PMID:35508546
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding. PMID:35501680
A new ChEMBL dataset for the similarity-based target fishing engine FastTargetPred: Annotation of an exhaustive list of linear tetrapeptides. PMID:35496477
An in silico pipeline for the discovery of multitarget ligands: A case study for epi-polypharmacology based on DNMT1/HDAC2 inhibition. PMID:35475037
A Consensus Compound/Bioactivity Dataset for Data-Driven Drug Design and Chemogenomics. PMID:35458710
GEOM, energy-annotated molecular conformations for property prediction and molecular generation. PMID:35449137
Discovery of moiety preference by Shapley value in protein kinase family using random forest models. PMID:35428180
Data-Driven Derivation of Molecular Substructures That Enhance Drug Activity in Gram-Negative Bacteria. PMID:35427114
Genomic Evidence Supports the Recognition of Endometriosis as an Inflammatory Systemic Disease and Reveals Disease-Specific Therapeutic Potentials of Targeting Neutrophil Degranulation. PMID:35401535
ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations. PMID:35379315
From pharmacogenetics to pharmaco-omics: Milestones and future directions. PMID:35373152
Azepine-Indole Alkaloids From Psychotria nemorosa Modulate 5-HT2A Receptors and Prevent in vivo Protein Toxicity in Transgenic Caenorhabditis elegans. PMID:35360162
Application of Transcriptomics for Predicting Protein Interaction Networks, Drug Targets and Drug Candidates. PMID:35356062
Ligand-based approaches to activity prediction for the early stage of structure-activity-relationship progression. PMID:35348984
Transformer-based molecular optimization beyond matched molecular pairs. PMID:35346368
NF-κB Signaling and Inflammation-Drug Repurposing to Treat Inflammatory Disorders? PMID:35336746
Therapeutic Targets for Heart Failure Identified Using Proteomics and Mendelian Randomization. PMID:35300523
Are we ready to design oral PROTACs®? PMID:35300370
A multitask GNN-based interpretable model for discovery of selective JAK inhibitors. PMID:35292114
Decomposing compounds enables reconstruction of interaction fingerprints for structure-based drug screening. PMID:35292113
Artificial Intelligent Deep Learning Molecular Generative Modeling of Scaffold-Focused and Cannabinoid CB2 Target-Specific Small-Molecule Sublibraries. PMID:35269537
Integrated Machine Learning and Chemoinformatics-Based Screening of Mycotic Compounds against Kinesin Spindle ProteinEg5 for Lung Cancer Therapy. PMID:35268740
AI-Driven Synthetic Route Design Incorporated with Retrosynthesis Knowledge. PMID:35258953
Predicting molecular initiating events using chemical target annotations and gene expression. PMID:35246223
PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. PMID:35227770
EMBER-Embedding Multiple Molecular Fingerprints for Virtual Screening. PMID:35216273
High-Throughput Chemical Screening and Structure-Based Models to Predict hERG Inhibition. PMID:35205076
Hydroxamic Acid as a Potent Metal-Binding Group for Inhibiting Tyrosinase. PMID:35204163
PTML Modeling for Pancreatic Cancer Research: In Silico Design of Simultaneous Multi-Protein and Multi-Cell Inhibitors. PMID:35203699
Predicting Antifouling Activity and Acetylcholinesterase Inhibition of Marine-Derived Compounds Using a Computer-Aided Drug Design Approach. PMID:35200658
Perplexity-Based Molecule Ranking and Bias Estimation of Chemical Language Models. PMID:35191696
A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer. PMID:35191375
Synthesis, Biological Evaluation and Molecular Docking Studies of 5-Indolylmethylen-4-oxo-2-thioxothiazolidine Derivatives. PMID:35164333
Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting Step. PMID:35163835
Unravelling Mechanisms of Doxorubicin-Induced Toxicity in 3D Human Intestinal Organoids. PMID:35163210
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
Drug-likeness scoring based on unsupervised learning. PMID:35126987
A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. PMID:35106508
The Brazilian compound library (BraCoLi) database: a repository of chemical and biological information for drug design. PMID:35089481
Candidates for Repurposing as Anti-Virulence Agents Based on the Structural Profile Analysis of Microbial Collagenase Inhibitors. PMID:35056958
Identification of miRNA-Small Molecule Associations by Continuous Feature Representation Using Auto-Encoders. PMID:35056899
Identifying FAAH Inhibitors as New Therapeutic Options for the Treatment of Chronic Pain through Drug Repurposing. PMID:35056095
A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. PMID:35037854
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet? PMID:35008685
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets. PMID:34986599
Machine Learning Enables Accurate and Rapid Prediction of Active Molecules Against Breast Cancer Cells. PMID:34975493
Mining Clinical Data for Novel Posttraumatic Stress Disorder Medications. PMID:34952698
New Inhibitors of Laccase and Tyrosinase by Examination of Cross-Inhibition between Copper-Containing Enzymes. PMID:34948458
Selection of Promising Novel Fragment Sized S. aureus SrtA Noncovalent Inhibitors Based on QSAR and Docking Modeling Studies. PMID:34946760
In Silico Drug Repurposing for Anti-Inflammatory Therapy: Virtual Search for Dual Inhibitors of Caspase-1 and TNF-Alpha. PMID:34944476
PreBINDS: An Interactive Web Tool to Create Appropriate Datasets for Predicting Compound-Protein Interactions. PMID:34938773
MODOMICS: a database of RNA modification pathways. 2021 update. PMID:34893873
IFPTML Mapping of Drug Graphs with Protein and Chromosome Structural Networks vs. Pre-Clinical Assay Information for Discovery of Antimalarial Compounds. PMID:34884870
Daily rhythms in gene expression of the human parasite Schistosoma mansoni. PMID:34852797
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases. PMID:34843456
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking. PMID:34825285
Development of a chemogenomics library for phenotypic screening. PMID:34819133
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. PMID:34788840
DeepH-DTA: Deep Learning for Predicting Drug-Target Interactions: A Case Study of COVID-19 Drug Repurposing. PMID:34786289
Identification of Novel Antagonists Targeting Cannabinoid Receptor 2 Using a Multi-Step Virtual Screening Strategy. PMID:34771087
Identification of potential pan-coronavirus therapies using a computational drug repurposing platform. PMID:34767922
Structure-based de novo drug design using 3D deep generative models. PMID:34760151
Priority index: database of genetic targets in immune-mediated disease. PMID:34751399
VARIDT 2.0: structural variability of drug transporter. PMID:34747471
Deep Learning Applied to Ligand-Based De Novo Drug Design. PMID:34731474
De Novo Molecular Design with Chemical Language Models. PMID:34731471
Deep Learning and Computational Chemistry. PMID:34731467
Applications of Artificial Intelligence in Drug Design: Opportunities and Challenges. PMID:34731463
Path4Drug: Data Science Workflow for Identification of Tissue-Specific Biological Pathways Modulated by Toxic Drugs. PMID:34721010
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials. PMID:34718737
The Natural Products Atlas 2.0: a database of microbially-derived natural products. PMID:34718710
Analysis of the uncharted, druglike property space by self-organizing maps. PMID:34709525
Curated Database and Preliminary AutoML QSAR Model for 5-HT1A Receptor. PMID:34684004
Validation of lipid-related therapeutic targets for coronary heart disease prevention using human genetics. PMID:34675202
Integrating heterogeneous data to facilitate COVID-19 drug repurposing. PMID:34666181
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. PMID:34648031
Individual and collective human intelligence in drug design: evaluating the search strategy. PMID:34635158
ABCpred: a webserver for the discovery of acetyl- and butyryl-cholinesterase inhibitors. PMID:34609711
Natural product scores and fingerprints extracted from artificial neural networks. PMID:34584636
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. PMID:34581813
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. PMID:34563271
A practical guide to large-scale docking. PMID:34561691
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling. PMID:34544485
Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. PMID:34519533
Accelerating antibiotic discovery through artificial intelligence. PMID:34504303
Congenericity of Claimed Compounds in Patent Applications. PMID:34500686
Computational Prediction of Compound-Protein Interactions for Orphan Targets Using CGBVS. PMID:34500569
Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease. PMID:34489936
Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. PMID:34472587
A data-driven methodology towards evaluating the potential of drug repurposing hypotheses. PMID:34471499
Will the chemical probes please stand up? PMID:34447939
Molecular Dynamics-Derived Pharmacophore Model Explaining the Nonselective Aspect of KV10.1 Pore Blockers. PMID:34445705
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Synthesis, In Silico and In Vitro Evaluation of Antimicrobial and Toxicity Features of New 4-[(4-Chlorophenyl)sulfonyl]benzoic Acid Derivatives. PMID:34443693
Synthesis and Biological Evaluation of New N-Acyl-α-amino Ketones and 1,3-Oxazoles Derivatives. PMID:34443608
Interpretation of Ligand-Based Activity Cliff Prediction Models Using the Matched Molecular Pair Kernel. PMID:34443503
Perturbation of ACE2 Structural Ensembles by SARS-CoV-2 Spike Protein Binding. PMID:34383488
Teaching a neural network to attach and detach electrons from molecules. PMID:34381051
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. PMID:34380569
Exploring Chemical Information in PubChem. PMID:34370395
Development of Machine Learning Models for Accurately Predicting and Ranking the Activity of Lead Molecules to Inhibit PRC2 Dependent Cancer. PMID:34358125
Prediction of antischistosomal small molecules using machine learning in the era of big data. PMID:34351547
In silico investigation to identify potential small molecule inhibitors of the RNA-dependent RNA polymerase (RdRp) nidovirus RdRp-associated nucleotidyltransferase domain. PMID:34305155
"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool. PMID:34301327
Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis. PMID:34285773
Structural binding site comparisons reveal Crizotinib as a novel LRRK2 inhibitor. PMID:34285770
The PROTACtable genome. PMID:34285415
Role of Plant-Derived Natural Compounds in Experimental Autoimmune Encephalomyelitis: A Review of the Treatment Potential and Development Strategy. PMID:34262447
Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review. PMID:34258685
Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design. PMID:34252946
Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals. PMID:34245241
Curated Data In - Trustworthy In Silico Models Out: The Impact of Data Quality on the Reliability of Artificial Intelligence Models as Alternatives to Animal Testing. PMID:34233495
A comprehensive review of integrative pharmacology-based investigation: A paradigm shift in traditional Chinese medicine. PMID:34221858
A Systems Approach to Brain Tumor Treatment. PMID:34202449
De novo Design of G Protein-Coupled Receptor 40 Peptide Agonists for Type 2 Diabetes Mellitus Based on Artificial Intelligence and Site-Directed Mutagenesis. PMID:34195182
Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. PMID:34193418
NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing. PMID:34188160
Bioactivity descriptors for uncharacterized chemical compounds. PMID:34168145
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Machine Learning Strategies When Transitioning between Biological Assays. PMID:34152755
Combining generative artificial intelligence and on-chip synthesis for de novo drug design. PMID:34117066
Illuminating elite patches of chemical space. PMID:34094392
Crowdsourced mapping of unexplored target space of kinase inhibitors. PMID:34083538
Evolution of kinase polypharmacology across HSP90 drug discovery. PMID:34077750
Synthesis and Anticancer Evaluation of New 1,3,4-Oxadiazole Derivatives. PMID:34066442
Discovery of Novel eEF2K Inhibitors Using HTS Fingerprint Generated from Predicted Profiling of Compound-Protein Interactions. PMID:34065377
DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal. PMID:34060634
Ranking-Oriented Quantitative Structure-Activity Relationship Modeling Combined with Assay-Wise Data Integration. PMID:34056351
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
Viral fibrotic scoring and drug screen based on MAPK activity uncovers EGFR as a key regulator of COVID-19 fibrosis. PMID:34045585
GABAB Receptor Chemistry and Pharmacology: Agonists, Antagonists, and Allosteric Modulators. PMID:34036555
Virtual screening for small molecular non-covalent binders of the SARS-CoV-2 main protease. PMID:34025857
Utilizing graph machine learning within drug discovery and development. PMID:34013350
Reconciling multiple connectivity scores for drug repurposing. PMID:34013329
Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation. PMID:34012976
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. PMID:33985583
Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies. PMID:33983732
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
SANCDB: an update on South African natural compounds and their readily available analogs. PMID:33952332
Target Prediction Model for Natural Products Using Transfer Learning. PMID:33924898
Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data. PMID:33923169
Deep Learning in Virtual Screening: Recent Applications and Developments. PMID:33922714
Ligand-Receptor Interactions and Machine Learning in GCGR and GLP-1R Drug Discovery. PMID:33920024
An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. PMID:33895786
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. PMID:33893803
Chemoinformatic Analysis of Psychotropic and Antihistaminic Drugs in the Light of Experimental Anti-SARS-CoV-2 Activities. PMID:33880039
Multisubstituted pyrimidines effectively inhibit bacterial growth and biofilm formation of Staphylococcus aureus. PMID:33846401
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
Actionable druggable genome-wide Mendelian randomization identifies repurposing opportunities for COVID-19. PMID:33837377
The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. PMID:33800393
The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment. PMID:33795932
Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons. PMID:33778899
Multiple Target Drug Design Using LigBuilder 3. PMID:33759133
Diversity oriented Deep Reinforcement Learning for targeted molecule generation. PMID:33750461
Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy. PMID:33746983
Integrating 3D structural information into systems biology. PMID:33744294
Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking. PMID:33739970
Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules: In silico studies. PMID:33716308
Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease. PMID:33672721
What is the role of cheminformatics in a pandemic? PMID:33653411
MAIP: a web service for predicting blood-stage malaria inhibitors. PMID:33618772
Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein. PMID:33603068
Single-cell RNA-seq dissects the intratumoral heterogeneity of triple-negative breast cancer based on gene regulatory networks. PMID:33575114
Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes. PMID:33573096
Current and prospective computational approaches and challenges for developing COVID-19 vaccines. PMID:33561453
Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay. PMID:33556646
De novo design and bioactivity prediction of SARS-CoV-2 main protease inhibitors using recurrent neural network-based transfer learning. PMID:33531083
Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening. PMID:33530327
Drug Safety Data Curation and Modeling in ChEMBL: Boxed Warnings and Withdrawn Drugs. PMID:33507738
An Integrated Approach to Identify New Anti-Filarial Leads to Treat River Blindness, a Neglected Tropical Disease. PMID:33466870
Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay. PMID:33446838
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. PMID:33436497
An open source chemical structure curation pipeline using RDKit. PMID:33431044
QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. PMID:33431038
Towards reproducible computational drug discovery. PMID:33430992
Reply to "Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery". PMID:33430932
Profiling and analysis of chemical compounds using pointwise mutual information. PMID:33423694
Bioinformatics: new tools and applications in life science and personalized medicine. PMID:33404829
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. PMID:33348379
Does tetanus vaccination contribute to reduced severity of the COVID-19 infection? PMID:33341328
Systematic mapping of cancer cell target dependencies using high-throughput drug screening in triple-negative breast cancer. PMID:33335681
No population left behind: Improving paediatric drug safety using informatics and systems biology. PMID:33332641
Structure-Based Virtual Screening of Ultra-Large Library Yields Potent Antagonists for a Lipid GPCR. PMID:33287369
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
GPCRdb in 2021: integrating GPCR sequence, structure and function. PMID:33270898
A Multi-Objective Approach for Anti-Osteosarcoma Cancer Agents Discovery through Drug Repurposing. PMID:33266378
Novel Small-Molecule Scaffolds as Candidates against the SARS Coronavirus 2 Main Protease: A Fragment-Guided in Silico Approach. PMID:33255326
A ligand-based computational drug repurposing pipeline using KNIME and Programmatic Data Access: case studies for rare diseases and COVID-19. PMID:33250934
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. PMID:33245775
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Moving targets in drug discovery. PMID:33214619
Cheminformatics to Characterize Pharmacologically Active Natural Products. PMID:33213003
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
Open Targets Platform: supporting systematic drug-target identification and prioritisation. PMID:33196847
Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment Through Hypothesis-Driven Systems Medicine Using CoVex. PMID:33164550
DrugCentral 2021 supports drug discovery and repositioning. PMID:33151287
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. PMID:33147627
A review on drug repurposing applicable to COVID-19. PMID:33147623
Perturbation-Theory Machine Learning (PTML) Multilabel Model of the ChEMBL Dataset of Preclinical Assays for Antisarcoma Compounds. PMID:33134682
MASI: microbiota-active substance interactions database. PMID:33125077
DrugSpaceX: a large screenable and synthetically tractable database extending drug space. PMID:33104791
Discovery of Potential Chemical Probe as Inhibitors of CXCL12 Using Ligand-Based Virtual Screening and Molecular Dynamic Simulation. PMID:33092204
KLIFS: an overhaul after the first 5 years of supporting kinase research. PMID:33084889
Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection. PMID:33083801
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors. PMID:33068433
Structural analysis of SARS-CoV-2 genome and predictions of the human interactome. PMID:33068416
StreptomeDB 3.0: an updated compendium of streptomycetes natural products. PMID:33051671
Computer-Aided Estimation of Biological Activity Profiles of Drug-Like Compounds Taking into Account Their Metabolism in Human Body. PMID:33050610
DockCoV2: a drug database against SARS-CoV-2. PMID:33035337
COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. PMID:33027420
PROTAC-DB: an online database of PROTACs. PMID:33010159
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Large-scale RNAi screening uncovers therapeutic targets in the parasite Schistosoma mansoni. PMID:32973031
Advances in Genomics for Drug Development. PMID:32824125
Predicting novel drugs for SARS-CoV-2 using machine learning from a >10 million chemical space. PMID:32802980
Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages. PMID:32730844
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters. PMID:32708318
Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis. PMID:32687148
Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs. PMID:32672454
Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing. PMID:32665542
Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. PMID:32663517
Drug mechanism-of-action discovery through the integration of pharmacological and CRISPR screens. PMID:32627965
Dr AFC: drug repositioning through anti-fibrosis characteristic. PMID:32572450
Anthelmintic drug discovery: target identification, screening methods and the role of open science. PMID:32550933
The Study on the hERG Blocker Prediction Using Chemical Fingerprint Analysis. PMID:32512802
iBioProVis: interactive visualization and analysis of compound bioactivity space. PMID:32407491
Drug Research Meets Network Science: Where Are We? PMID:32338900
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. PMID:32297936
Opening up connectivity between documents, structures and bioactivity. PMID:32280387
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. PMID:32187356
The exposome and health: Where chemistry meets biology. PMID:31974245
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. PMID:31971579
In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. PMID:31970149
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities. PMID:31783634
Trypanocidal Mechanism of Action and in silico Studies of p-Coumaric Acid Derivatives. PMID:31775321
An omics perspective on drug target discovery platforms. PMID:31774113
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. PMID:31691823
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration. PMID:31680154
VARIDT 1.0: variability of drug transporter database. PMID:31495872
Cardioprotective Melatonin: Translating from Proof-of-Concept Studies to Therapeutic Use. PMID:31491852
Applicability Domain of Active Learning in Chemical Probe Identification: Convergence in Learning from Non-Specific Compounds and Decision Rule Clarification. PMID:31357419
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. PMID:31106366
Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery. PMID:30631996
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr PubMed citations: 59.

59 articles citing: ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr

Artificial intelligence and machine-learning approaches in structure and ligand-based discovery of drugs affecting central nervous system. PMID:35819579
Computational Drug Repurposing for Antituberculosis Therapy: Discovery of Multi-Strain Inhibitors. PMID:34439055
Computational Approaches in Preclinical Studies on Drug Discovery and Development. PMID:33062633
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening. PMID:29306979
Fragment-based in silico modeling of multi-target inhibitors against breast cancer-related proteins. PMID:28194627
Large-scale ligand-based predictive modelling using support vector machines. PMID:27516811
Biocuration with insufficient resources and fixed timelines. PMID:26708987
Molecular Mechanism of Action of Triazolobenzodiazepinone Agonists of the Type 1 Cholecystokinin Receptor. Possible Cooperativity across the Receptor Homodimeric Complex. PMID:26654202
The Recognition of Identical Ligands by Unrelated Proteins. PMID:26421501
Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26-27 June 2013, Research Triangle Park, NC, USA. PMID:25326818
Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding. PMID:25319540
Dual-target virtual screening by pharmacophore elucidation and molecular shape filtering. PMID:24900445
Chemical structure identification in metabolomics: computational modeling of experimental features. PMID:24688698
Integrated text mining and chemoinformatics analysis associates diet to health benefit at molecular level. PMID:24453957
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
Comparative analyses of lipoprotein lipase, hepatic lipase, and endothelial lipase, and their binding properties with known inhibitors. PMID:23991054
How Far Could We Go with Open Data - A Case Study for TRPV1 Antagonists. PMID:23956804
Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile. PMID:23840562
Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor. PMID:23754289
The ChEMBL database as linked open data. PMID:23657106
Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. PMID:23509259
BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space. PMID:23330685
Exploring chemical space for drug discovery using the chemical universe database. PMID:23019491
Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain. PMID:22959526
High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. PMID:22932902
IUPHAR-DB: an open-access, expert-curated resource for receptor and ion channel research. PMID:22778867
A two-step target binding and selectivity support vector machines approach for virtual screening of dopamine receptor subtype-selective ligands. PMID:22720033
Life beyond kinases: structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors. PMID:22694093
A framework for mapping, visualisation and automatic model creation of signal-transduction networks. PMID:22531118
Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor. PMID:22467877
Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis. PMID:22432004
In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. PMID:22373185
ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis. PMID:22345505
Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. PMID:22339582
Predicting the mechanism of phospholipidosis. PMID:22281160
Global analysis of small molecule binding to related protein targets. PMID:22253582
Whole-genome sequence of Schistosoma haematobium. PMID:22246508
Self-organizing ontology of biochemically relevant small molecules. PMID:22221313
Using multiple microenvironments to find similar ligand-binding sites: application to kinase inhibitor binding. PMID:22219723
Understanding and classifying metabolite space and metabolite-likeness. PMID:22194963
Can we really do computer-aided drug design? PMID:22160553
SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. PMID:22067445
Pharmacophore-based discovery of FXR agonists. Part I: Model development and experimental validation. PMID:22018919
Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor. PMID:22007643
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. PMID:21999342
The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PMID:21991315
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. PMID:21948793
ChEMBL: a large-scale bioactivity database for drug discovery. PMID:21948594
Structural diversity of biologically interesting datasets: a scaffold analysis approach. PMID:21824432
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Theoretical study of GSK-3α: neural networks QSAR studies for the design of new inhibitors using 2D descriptors. PMID:21735119
Software and resources for computational medicinal chemistry. PMID:21707404
Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem. PMID:21618008
Guiding effective decisions: an interview with Matthew Segall, CEO of Optibrium. Interview by Wendy A. Warr. PMID:21225445
Reactome: a database of reactions, pathways and biological processes. PMID:21067998
The chemical basis of pharmacology. PMID:21058655
ASD: a comprehensive database of allosteric proteins and modulators. PMID:21051350
PubChem as a public resource for drug discovery. PMID:20970519
Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PMID:20808766

http://europepmc.org/articles/PMC5210557

http://dx.doi.org/10.1093/nar/gkt1031

http://dx.doi.org/10.1093/nar/gkv1352

Tags:

Tags
More detailed information about this field from each metasource.

bioactivity
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

chemical entity
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

chemical structure
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

drug
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

tissue
metasource: Fairsharing.org
version: FAIRsharing.org: ChEMBL; ChEMBL; DOI: https://doi.org/10.25504/FAIRsharing.m3jtpg; Last edited: March 8, 2021, 10:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

other molecular biology databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

drugs and drug design
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

basic research
metasource: re3data.org
version: re3data.org: ChEMBL; editing status 2021-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C320 last accessed: 2022-11-04

life science experiments
metasource: re3data.org
version: re3data.org: ChEMBL; editing status 2021-12-14; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3C320 last accessed: 2022-11-04

small molecules
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

chemical biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

cheminformatics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

bioactivity chemical entity chemical structure drug genome small molecule tissue molecular biology drug basic research life science experiments small molecule chemical biology cheminformatics

More to explore:

1/20

Previous Next

Need help integrating and/or managing biomedical data?

Webpage:

Licence:

More to explore:

1/20

Drug2Gene

IUPHAR/BPS Guide to PHARMACOLOGY

BioModels

BindingDB database of measured binding affinities

HybridMolDB

TTD, Therapeutic Target Database

Probes and Drugs

Manually Curated Database of Rice Proteins

Database of Genomic Variants archive (DGVa)

The European Bioinformatics Institute Tools

Chemical Component Dictionary

Pharmacogenomics Knowledge Base

Chemical Entities of Biological Interest

BioStudies

canSAR

TDR Targets

DrugCentral

The UC Irvine ChemDB

Complex Portal

DrugBank